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Output file from fmriprep
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| Sat Jan 19 13:11:25 AEDT 2019 | |
| /data/cephfs/punim0752/fmriprep | |
| fmriprep_test | |
| 1 | |
| subject number: 01 | |
| running... singularity run --cleanenv -B /data/cephfs/punim0752/fmriprep:/data/cephfs/punim0752/fmriprep /data/cephfs/punim0752/fmriprep/fmriprep_image/fmriprep-1.2.5.simg /data/cephfs/punim0752/fmriprep/orwa_5subs/orwa_1sub_4cpus/orwa_BIDS /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/ participant --participant-label sub-01 --nthreads 1 --n_cpus 4 --fs-license-file /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/license.txt --use-aroma | |
| [32mThis dataset appears to be BIDS compatible.[39m | |
| [34m[4mSummary:[24m[39m [34m[4mAvailable Tasks:[24m[39m [34m[4mAvailable Modalities:[24m[39m | |
| 5 Files, 175.38MB rest T1w | |
| 1 - Subject bold | |
| 1 - Session | |
| [37mIf you have any questions please post on https://neurostars.org/tags/bids[39m | |
| Making sure the input data is BIDS compliant (warnings can be ignored in most cases). | |
| 190119-02:11:46,606 nipype.workflow IMPORTANT: | |
| Running fMRIPREP version 1.2.5: | |
| * BIDS dataset path: /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS. | |
| * Participant list: ['01']. | |
| * Run identifier: 20190119-021146_544e3481-dffd-44d7-9510-63b7161b80d6. | |
| 190119-02:11:49,377 nipype.workflow IMPORTANT: | |
| Creating bold processing workflow for "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.nii" (0.09 GB / 510 TRs). Memory resampled/largemem=0.37/0.85 GB. | |
| 190119-02:11:49,378 nipype.workflow IMPORTANT: | |
| No single-band-reference found for sub-01_task-rest_bold.nii | |
| 190119-02:11:53,700 nipype.workflow IMPORTANT: | |
| Slice-timing correction will be included. | |
| 190119-02:11:53,738 nipype.workflow WARNING: | |
| SDC: no fieldmaps found or they were ignored (/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.nii). | |
| 190119-02:11:55,86 nipype.workflow IMPORTANT: | |
| Creating BOLD surface-sampling workflow. | |
| 190119-02:12:01,764 nipype.workflow IMPORTANT: | |
| Works derived from this fMRIPrep execution should include the following boilerplate: | |
| Results included in this manuscript come from preprocessing | |
| performed using *fMRIPprep* 1.2.5 | |
| (@fmriprep1; @fmriprep2; RRID:SCR_016216), | |
| which is based on *Nipype* 1.1.6 | |
| (@nipype1; @nipype2; RRID:SCR_002502). | |
| Anatomical data preprocessing | |
| : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) | |
| using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0], | |
| and used as T1w-reference throughout the workflow. | |
| The T1w-reference was then skull-stripped using `antsBrainExtraction.sh` | |
| (ANTs 2.2.0), using OASIS as target template. | |
| Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1, | |
| RRID:SCR_001847, @fs_reconall], and the brain mask estimated | |
| previously was refined with a custom variation of the method to reconcile | |
| ANTs-derived and FreeSurfer-derived segmentations of the cortical | |
| gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle]. | |
| Spatial normalization to the ICBM 152 Nonlinear Asymmetrical | |
| template version 2009c [@mni, RRID:SCR_008796] was performed | |
| through nonlinear registration with `antsRegistration` | |
| [ANTs 2.2.0, RRID:SCR_004757, @ants], using | |
| brain-extracted versions of both T1w volume and template. | |
| Brain tissue segmentation of cerebrospinal fluid (CSF), | |
| white-matter (WM) and gray-matter (GM) was performed on | |
| the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823, | |
| @fsl_fast]. | |
| Functional data preprocessing | |
| : For each of the 1 BOLD runs found per subject (across all | |
| tasks and sessions), the following preprocessing was performed. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| The BOLD reference was then co-registered to the T1w reference using | |
| `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. | |
| Co-registration was configured with nine degrees of freedom to account | |
| for distortions remaining in the BOLD reference. | |
| Head-motion parameters with respect to the BOLD reference | |
| (transformation matrices, and six corresponding rotation and translation | |
| parameters) are estimated before any spatiotemporal filtering using | |
| `mcflirt` [FSL 5.0.9, @mcflirt]. | |
| BOLD runs were slice-time corrected using `3dTshift` from | |
| AFNI 20160207 [@afni, RRID:SCR_005927]. | |
| The BOLD time-series, were resampled to surfaces on the following | |
| spaces: *fsaverage5*. | |
| The BOLD time-series (including slice-timing correction when applied) | |
| were resampled onto their original, native space by applying | |
| a single, composite transform to correct for head-motion and | |
| susceptibility distortions. | |
| These resampled BOLD time-series will be referred to as *preprocessed | |
| BOLD in original space*, or just *preprocessed BOLD*. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| Automatic removal of motion artifacts using independent component analysis | |
| [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* | |
| time-series after removal of non-steady state volumes and spatial smoothing | |
| with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). | |
| Corresponding "non-aggresively" denoised runs were produced after such | |
| smoothing. | |
| Additionally, the "aggressive" noise-regressors were collected and placed | |
| in the corresponding confounds file. | |
| The BOLD time-series were resampled to MNI152NLin2009cAsym standard space, | |
| generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| Several confounding time-series were calculated based on the | |
| *preprocessed BOLD*: framewise displacement (FD), DVARS and | |
| three region-wise global signals. | |
| FD and DVARS are calculated for each functional run, both using their | |
| implementations in *Nipype* [following the definitions by @power_fd_dvars]. | |
| The three global signals are extracted within the CSF, the WM, and | |
| the whole-brain masks. | |
| Additionally, a set of physiological regressors were extracted to | |
| allow for component-based noise correction [*CompCor*, @compcor]. | |
| Principal components are estimated after high-pass filtering the | |
| *preprocessed BOLD* time-series (using a discrete cosine filter with | |
| 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) | |
| and anatomical (aCompCor). | |
| Six tCompCor components are then calculated from the top 5% variable | |
| voxels within a mask covering the subcortical regions. | |
| This subcortical mask is obtained by heavily eroding the brain mask, | |
| which ensures it does not include cortical GM regions. | |
| For aCompCor, six components are calculated within the intersection of | |
| the aforementioned mask and the union of CSF and WM masks calculated | |
| in T1w space, after their projection to the native space of each | |
| functional run (using the inverse BOLD-to-T1w transformation). | |
| The head-motion estimates calculated in the correction step were also | |
| placed within the corresponding confounds file. | |
| All resamplings can be performed with *a single interpolation | |
| step* by composing all the pertinent transformations (i.e. head-motion | |
| transform matrices, susceptibility distortion correction when available, | |
| and co-registrations to anatomical and template spaces). | |
| Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), | |
| configured with Lanczos interpolation to minimize the smoothing | |
| effects of other kernels [@lanczos]. | |
| Non-gridded (surface) resamplings were performed using `mri_vol2surf` | |
| (FreeSurfer). | |
| Many internal operations of *fMRIPrep* use | |
| *Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362], | |
| mostly within the functional processing workflow. | |
| For more details of the pipeline, see [the section corresponding | |
| to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation"). | |
| ### References | |
| [WARNING] This document format requires a nonempty <title> element. | |
| Please specify either 'title' or 'pagetitle' in the metadata. | |
| Falling back to 'CITATION' | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| imp.find_module('pytest') | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/dataset_description.json' mode='r' encoding='UTF-8'> | |
| self.description = json.load(open(target, 'r')) | |
| /usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/config/bids.json' mode='r' encoding='UTF-8'> | |
| domain = json.load(open(domain, 'r')) | |
| /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.json' mode='r' encoding='utf-8'> | |
| encoding='utf-8')) | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| imp.find_module('pytest') | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| 190119-02:12:27,621 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate". | |
| 190119-02:12:27,705 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/bidssrc". | |
| 190119-02:12:27,991 nipype.workflow INFO: | |
| [Node] Running "bidssrc" ("fmriprep.interfaces.bids.BIDSDataGrabber") | |
| 190119-02:12:27,997 nipype.interface WARNING: | |
| No 't2w' images found for sub-<undefined> | |
| 190119-02:12:27,997 nipype.interface WARNING: | |
| No 'flair' images found for sub-<undefined> | |
| 190119-02:12:27,998 nipype.interface WARNING: | |
| No 'fmap' images found for sub-<undefined> | |
| 190119-02:12:27,998 nipype.interface WARNING: | |
| No 'sbref' images found for sub-<undefined> | |
| 190119-02:12:27,999 nipype.interface WARNING: | |
| No 'roi' images found for sub-<undefined> | |
| 190119-02:12:28,26 nipype.workflow INFO: | |
| [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-02:12:28,199 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc". | |
| 190119-02:12:30,11 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate". | |
| Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| 190119-02:12:59,789 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref". | |
| 190119-02:13:00,182 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 190119-02:13:00,445 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". | |
| 190119-02:13:00,623 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref". | |
| 190119-02:13:01,75 nipype.workflow INFO: | |
| [Node] Running "t1_template_dimensions" ("fmriprep.interfaces.images.TemplateDimensions") | |
| 190119-02:13:01,376 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". | |
| 190119-02:13:01,507 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction". | |
| 190119-02:13:01,528 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref". | |
| 190119-02:13:02,307 nipype.workflow INFO: | |
| [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-02:13:02,611 nipype.workflow INFO: | |
| [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: | |
| 3dTshift -ignore 1 -prefix sub-01_task-rest_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 1.4s /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction/sub-01_task-rest_bold_valid.nii | |
| 190119-02:13:03,142 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref". | |
| 190119-02:13:05,696 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". | |
| 190119-02:13:05,838 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform". | |
| 190119-02:13:05,925 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt". | |
| 190119-02:13:06,324 nipype.workflow INFO: | |
| [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") | |
| 190119-02:13:06,344 nipype.workflow INFO: | |
| [Node] Setting-up "_t1_conform0" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". | |
| 190119-02:13:06,501 nipype.workflow INFO: | |
| [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: | |
| mcflirt -in /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-01_task-rest_bold_valid.nii -out /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-01_task-rest_bold_valid_mcf.nii.gz -reffile /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz -mats -plots | |
| 190119-02:13:06,846 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". | |
| 190119-02:13:07,80 nipype.workflow INFO: | |
| [Node] Running "_t1_conform0" ("fmriprep.interfaces.images.Conform") | |
| 190119-02:13:13,330 nipype.workflow INFO: | |
| [Node] Finished "_t1_conform0". | |
| 190119-02:13:13,525 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform". | |
| 190119-02:13:14,365 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config". | |
| 190119-02:13:14,784 nipype.workflow INFO: | |
| [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs") | |
| 190119-02:13:15,11 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config". | |
| 190119-02:13:27,166 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction". | |
| 190119-02:13:27,921 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform". | |
| 190119-02:13:28,107 nipype.workflow INFO: | |
| [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:13:32,945 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform". | |
| 190119-02:13:33,932 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_split" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_split". | |
| 190119-02:13:34,138 nipype.workflow INFO: | |
| [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: | |
| fslsplit /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform/sub-01_task-rest_bold_valid_tshift_xform.nii.gz -t | |
| 190119-02:14:30,198 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_split". | |
| 190119-02:14:32,698 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/ica_aroma_wf/bold_mni_trans_wf/gen_ref". | |
| 190119-02:14:33,134 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 190119-02:14:33,353 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref". | |
| 190119-02:14:33,643 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 190119-02:14:34,87 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref". | |
| 190119-02:14:34,247 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref". | |
| 190119-02:14:35,981 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". | |
| 190119-02:14:36,175 nipype.workflow INFO: | |
| [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: | |
| antsAI -c [10,0.000001,10] -d 3 -x /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 | |
| 190119-02:14:49,595 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". | |
| 190119-02:14:50,154 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". | |
| 190119-02:14:50,415 nipype.workflow INFO: | |
| [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 | |
| 190119-02:14:55,387 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". | |
| 190119-02:14:56,314 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". | |
| 190119-02:14:56,443 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] | |
| 190119-02:15:01,159 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". | |
| 190119-02:15:02,38 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". | |
| 190119-02:15:02,245 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz | |
| 190119-02:15:03,27 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". | |
| 190119-02:15:04,123 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 190119-02:15:04,405 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip". | |
| 190119-02:15:04,539 nipype.workflow INFO: | |
| [Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command: | |
| antsBrainExtraction.sh -a /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii -m /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/tpl-OASIS30ANTs_res-01_class-brainmask_probtissue.nii.gz -e /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz -d 3 -f /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BrainCerebellumExtraction_roi.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1 | |
| 190119-02:15:21,735 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt". | |
| 190119-02:15:24,865 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". | |
| 190119-02:15:24,981 nipype.workflow INFO: | |
| [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") | |
| 190119-02:15:25,139 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion". | |
| 190119-02:15:26,450 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp". | |
| 190119-02:15:26,502 nipype.workflow INFO: | |
| [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 190119-02:15:26,623 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp". | |
| 190119-02:15:28,43 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". | |
| 190119-02:15:28,127 nipype.workflow INFO: | |
| [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz | |
| 190119-02:15:30,318 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". | |
| 190119-02:15:32,49 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". | |
| 190119-02:15:32,155 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m | |
| 190119-02:15:34,533 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". | |
| 190119-02:15:36,18 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". | |
| 190119-02:15:36,65 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz | |
| 190119-02:15:36,495 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". | |
| 190119-02:15:38,53 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". | |
| 190119-02:15:38,96 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-02:15:38,547 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". | |
| 190119-02:15:40,58 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". | |
| 190119-02:15:40,128 nipype.workflow INFO: | |
| [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: | |
| 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-02:15:42,64 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". | |
| 190119-02:15:44,104 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". | |
| 190119-02:15:44,150 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:15:44,439 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". | |
| 190119-02:15:46,35 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". | |
| 190119-02:15:46,90 nipype.workflow INFO: | |
| [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: | |
| 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz | |
| 190119-02:15:46,834 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". | |
| 190119-02:15:48,55 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". | |
| 190119-02:15:48,89 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:15:48,216 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". | |
| 190119-02:15:50,46 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". | |
| 190119-02:15:50,88 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz | |
| 190119-02:15:50,488 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". | |
| 190119-02:15:52,52 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". | |
| 190119-02:15:52,94 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz | |
| 190119-02:15:52,610 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". | |
| 190119-03:31:29,296 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip". | |
| 190119-03:31:40,822 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". | |
| 190119-03:31:42,513 nipype.workflow INFO: | |
| [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK") | |
| 190119-03:34:22,874 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk". | |
| 190119-03:34:25,526 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1". | |
| 190119-03:34:25,801 nipype.workflow INFO: | |
| [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon1 -i /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii -noskullstrip -hires -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer -expert /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts | |
| 190119-13:45:38,968 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1". | |
| 190119-13:45:48,355 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm". | |
| 190119-13:45:48,558 nipype.workflow INFO: | |
| [Node] Running "fsnative_2_t1_xfm" ("fmriprep.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command: | |
| mri_robust_register --satit --iscale --lta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer/sub-01/mri/T1.mgz --dst /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii | |
| 190119-13:45:48,983 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_transform". | |
| 190119-13:45:50,540 nipype.workflow INFO: | |
| [Node] Running "bold_transform" ("fmriprep.interfaces.itk.MultiApplyTransforms") | |
| 190119-13:52:34,378 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform". | |
| 190119-13:52:41,799 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". | |
| 190119-13:52:42,77 nipype.workflow INFO: | |
| [Node] Running "skull_strip_extern" ("fmriprep.interfaces.freesurfer.FSInjectBrainExtracted") | |
| 190119-13:52:42,545 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge". | |
| 190119-13:52:44,138 nipype.workflow INFO: | |
| [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") | |
| 190119-13:53:16,404 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". | |
| 190119-13:54:11,429 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge". | |
| 190119-13:54:12,86 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate". | |
| 190119-13:54:12,333 nipype.workflow INFO: | |
| [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-13:54:18,788 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate". | |
| 190119-13:54:20,78 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". | |
| 190119-13:54:20,248 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 190119-13:54:20,803 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". | |
| 190119-13:54:22,70 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref". | |
| 190119-13:54:22,229 nipype.workflow INFO: | |
| [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-13:54:22,899 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref". | |
| 190119-13:54:24,71 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". | |
| 190119-13:54:24,279 nipype.workflow INFO: | |
| [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: | |
| antsAI -c [10,0.000001,10] -d 3 -x /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 | |
| 190119-13:54:39,216 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". | |
| 190119-13:54:40,155 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". | |
| 190119-13:54:40,327 nipype.workflow INFO: | |
| [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 | |
| 190119-13:54:43,483 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". | |
| 190119-13:54:44,128 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". | |
| 190119-13:54:44,296 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] | |
| 190119-13:54:47,254 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". | |
| 190119-13:54:48,145 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". | |
| 190119-13:54:48,307 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz | |
| 190119-13:54:49,48 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". | |
| 190119-13:54:50,348 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 190119-13:54:50,946 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". | |
| 190119-13:54:51,199 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:54:51,228 nipype.workflow INFO: | |
| [Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:54:51,245 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:55:11,693 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm". | |
| 190119-13:55:12,175 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". | |
| 190119-13:55:12,343 nipype.workflow INFO: | |
| [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz | |
| 190119-13:55:14,130 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". | |
| 190119-13:55:16,144 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". | |
| 190119-13:55:16,317 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m | |
| 190119-13:55:19,344 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". | |
| 190119-13:55:20,135 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". | |
| 190119-13:55:20,335 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz | |
| 190119-13:55:21,194 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". | |
| 190119-13:55:22,187 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". | |
| 190119-13:55:22,520 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-13:55:23,252 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". | |
| 190119-13:55:24,149 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". | |
| 190119-13:55:24,403 nipype.workflow INFO: | |
| [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: | |
| 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-13:55:31,776 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". | |
| 190119-13:55:32,162 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". | |
| 190119-13:55:32,309 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-13:55:32,926 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". | |
| 190119-13:55:34,156 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". | |
| 190119-13:55:34,570 nipype.workflow INFO: | |
| [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: | |
| 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz | |
| 190119-13:55:42,157 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". | |
| 190119-13:55:44,230 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". | |
| 190119-13:55:44,549 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-13:55:45,151 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". | |
| 190119-13:55:46,214 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". | |
| 190119-13:55:46,628 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz | |
| 190119-13:55:47,201 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". | |
| 190119-13:55:48,202 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_confounds_wf/dvars". | |
| 190119-13:55:48,585 nipype.workflow INFO: | |
| [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 190119-13:56:02,351 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars". | |
| 190119-13:56:06,330 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". | |
| 190119-13:56:06,890 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz | |
| 190119-13:56:07,697 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". | |
| 190119-13:56:08,606 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm". | |
| 190119-13:56:08,938 nipype.workflow INFO: | |
| [Node] Running "t1_2_fsnative_xfm" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta | |
| 190119-13:56:09,607 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm". | |
| 190119-13:56:10,548 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk". | |
| 190119-13:56:11,120 nipype.workflow INFO: | |
| [Node] Running "lta_2_itk" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt | |
| 190119-13:56:11,672 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk". | |
| slurmstepd: error: *** JOB 7250036 ON spartan-rc156 CANCELLED AT 2019-01-20T14:11:51 DUE TO TIME LIMIT *** |
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| Sat Jan 19 13:11:25 AEDT 2019 | |
| /data/cephfs/punim0752/fmriprep | |
| fmriprep_test | |
| 1 | |
| subject number: 01 | |
| running... singularity run --cleanenv -B /data/cephfs/punim0752/fmriprep:/data/cephfs/punim0752/fmriprep /data/cephfs/punim0752/fmriprep/fmriprep_image/fmriprep-1.2.5.simg /data/cephfs/punim0752/fmriprep/orwa_5subs/orwa_1sub_4cpus/orwa_BIDS /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/ participant --participant-label sub-01 --nthreads 1 --n_cpus 4 --fs-license-file /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/license.txt --use-aroma | |
| [32mThis dataset appears to be BIDS compatible.[39m | |
| [34m[4mSummary:[24m[39m [34m[4mAvailable Tasks:[24m[39m [34m[4mAvailable Modalities:[24m[39m | |
| 5 Files, 175.38MB rest T1w | |
| 1 - Subject bold | |
| 1 - Session | |
| [37mIf you have any questions please post on https://neurostars.org/tags/bids[39m | |
| Making sure the input data is BIDS compliant (warnings can be ignored in most cases). | |
| 190119-02:11:46,606 nipype.workflow IMPORTANT: | |
| Running fMRIPREP version 1.2.5: | |
| * BIDS dataset path: /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS. | |
| * Participant list: ['01']. | |
| * Run identifier: 20190119-021146_544e3481-dffd-44d7-9510-63b7161b80d6. | |
| 190119-02:11:49,377 nipype.workflow IMPORTANT: | |
| Creating bold processing workflow for "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.nii" (0.09 GB / 510 TRs). Memory resampled/largemem=0.37/0.85 GB. | |
| 190119-02:11:49,378 nipype.workflow IMPORTANT: | |
| No single-band-reference found for sub-01_task-rest_bold.nii | |
| 190119-02:11:53,700 nipype.workflow IMPORTANT: | |
| Slice-timing correction will be included. | |
| 190119-02:11:53,738 nipype.workflow WARNING: | |
| SDC: no fieldmaps found or they were ignored (/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.nii). | |
| 190119-02:11:55,86 nipype.workflow IMPORTANT: | |
| Creating BOLD surface-sampling workflow. | |
| 190119-02:12:01,764 nipype.workflow IMPORTANT: | |
| Works derived from this fMRIPrep execution should include the following boilerplate: | |
| Results included in this manuscript come from preprocessing | |
| performed using *fMRIPprep* 1.2.5 | |
| (@fmriprep1; @fmriprep2; RRID:SCR_016216), | |
| which is based on *Nipype* 1.1.6 | |
| (@nipype1; @nipype2; RRID:SCR_002502). | |
| Anatomical data preprocessing | |
| : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) | |
| using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0], | |
| and used as T1w-reference throughout the workflow. | |
| The T1w-reference was then skull-stripped using `antsBrainExtraction.sh` | |
| (ANTs 2.2.0), using OASIS as target template. | |
| Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1, | |
| RRID:SCR_001847, @fs_reconall], and the brain mask estimated | |
| previously was refined with a custom variation of the method to reconcile | |
| ANTs-derived and FreeSurfer-derived segmentations of the cortical | |
| gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle]. | |
| Spatial normalization to the ICBM 152 Nonlinear Asymmetrical | |
| template version 2009c [@mni, RRID:SCR_008796] was performed | |
| through nonlinear registration with `antsRegistration` | |
| [ANTs 2.2.0, RRID:SCR_004757, @ants], using | |
| brain-extracted versions of both T1w volume and template. | |
| Brain tissue segmentation of cerebrospinal fluid (CSF), | |
| white-matter (WM) and gray-matter (GM) was performed on | |
| the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823, | |
| @fsl_fast]. | |
| Functional data preprocessing | |
| : For each of the 1 BOLD runs found per subject (across all | |
| tasks and sessions), the following preprocessing was performed. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| The BOLD reference was then co-registered to the T1w reference using | |
| `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. | |
| Co-registration was configured with nine degrees of freedom to account | |
| for distortions remaining in the BOLD reference. | |
| Head-motion parameters with respect to the BOLD reference | |
| (transformation matrices, and six corresponding rotation and translation | |
| parameters) are estimated before any spatiotemporal filtering using | |
| `mcflirt` [FSL 5.0.9, @mcflirt]. | |
| BOLD runs were slice-time corrected using `3dTshift` from | |
| AFNI 20160207 [@afni, RRID:SCR_005927]. | |
| The BOLD time-series, were resampled to surfaces on the following | |
| spaces: *fsaverage5*. | |
| The BOLD time-series (including slice-timing correction when applied) | |
| were resampled onto their original, native space by applying | |
| a single, composite transform to correct for head-motion and | |
| susceptibility distortions. | |
| These resampled BOLD time-series will be referred to as *preprocessed | |
| BOLD in original space*, or just *preprocessed BOLD*. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| Automatic removal of motion artifacts using independent component analysis | |
| [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* | |
| time-series after removal of non-steady state volumes and spatial smoothing | |
| with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). | |
| Corresponding "non-aggresively" denoised runs were produced after such | |
| smoothing. | |
| Additionally, the "aggressive" noise-regressors were collected and placed | |
| in the corresponding confounds file. | |
| The BOLD time-series were resampled to MNI152NLin2009cAsym standard space, | |
| generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*. | |
| First, a reference volume and its skull-stripped version were generated | |
| using a custom methodology of *fMRIPrep*. | |
| Several confounding time-series were calculated based on the | |
| *preprocessed BOLD*: framewise displacement (FD), DVARS and | |
| three region-wise global signals. | |
| FD and DVARS are calculated for each functional run, both using their | |
| implementations in *Nipype* [following the definitions by @power_fd_dvars]. | |
| The three global signals are extracted within the CSF, the WM, and | |
| the whole-brain masks. | |
| Additionally, a set of physiological regressors were extracted to | |
| allow for component-based noise correction [*CompCor*, @compcor]. | |
| Principal components are estimated after high-pass filtering the | |
| *preprocessed BOLD* time-series (using a discrete cosine filter with | |
| 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) | |
| and anatomical (aCompCor). | |
| Six tCompCor components are then calculated from the top 5% variable | |
| voxels within a mask covering the subcortical regions. | |
| This subcortical mask is obtained by heavily eroding the brain mask, | |
| which ensures it does not include cortical GM regions. | |
| For aCompCor, six components are calculated within the intersection of | |
| the aforementioned mask and the union of CSF and WM masks calculated | |
| in T1w space, after their projection to the native space of each | |
| functional run (using the inverse BOLD-to-T1w transformation). | |
| The head-motion estimates calculated in the correction step were also | |
| placed within the corresponding confounds file. | |
| All resamplings can be performed with *a single interpolation | |
| step* by composing all the pertinent transformations (i.e. head-motion | |
| transform matrices, susceptibility distortion correction when available, | |
| and co-registrations to anatomical and template spaces). | |
| Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), | |
| configured with Lanczos interpolation to minimize the smoothing | |
| effects of other kernels [@lanczos]. | |
| Non-gridded (surface) resamplings were performed using `mri_vol2surf` | |
| (FreeSurfer). | |
| Many internal operations of *fMRIPrep* use | |
| *Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362], | |
| mostly within the functional processing workflow. | |
| For more details of the pipeline, see [the section corresponding | |
| to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation"). | |
| ### References | |
| [WARNING] This document format requires a nonempty <title> element. | |
| Please specify either 'title' or 'pagetitle' in the metadata. | |
| Falling back to 'CITATION' | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| imp.find_module('pytest') | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/dataset_description.json' mode='r' encoding='UTF-8'> | |
| self.description = json.load(open(target, 'r')) | |
| /usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/config/bids.json' mode='r' encoding='UTF-8'> | |
| domain = json.load(open(domain, 'r')) | |
| /usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_BIDS/sub-01/func/sub-01_task-rest_bold.json' mode='r' encoding='utf-8'> | |
| encoding='utf-8')) | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'> | |
| imp.find_module('pytest') | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| /usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| 190119-02:12:27,621 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate". | |
| 190119-02:12:27,705 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/bidssrc". | |
| 190119-02:12:27,991 nipype.workflow INFO: | |
| [Node] Running "bidssrc" ("fmriprep.interfaces.bids.BIDSDataGrabber") | |
| 190119-02:12:27,997 nipype.interface WARNING: | |
| No 't2w' images found for sub-<undefined> | |
| 190119-02:12:27,997 nipype.interface WARNING: | |
| No 'flair' images found for sub-<undefined> | |
| 190119-02:12:27,998 nipype.interface WARNING: | |
| No 'fmap' images found for sub-<undefined> | |
| 190119-02:12:27,998 nipype.interface WARNING: | |
| No 'sbref' images found for sub-<undefined> | |
| 190119-02:12:27,999 nipype.interface WARNING: | |
| No 'roi' images found for sub-<undefined> | |
| 190119-02:12:28,26 nipype.workflow INFO: | |
| [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-02:12:28,199 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc". | |
| 190119-02:12:30,11 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate". | |
| Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| 190119-02:12:59,789 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref". | |
| 190119-02:13:00,182 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 190119-02:13:00,445 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". | |
| 190119-02:13:00,623 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref". | |
| 190119-02:13:01,75 nipype.workflow INFO: | |
| [Node] Running "t1_template_dimensions" ("fmriprep.interfaces.images.TemplateDimensions") | |
| 190119-02:13:01,376 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". | |
| 190119-02:13:01,507 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction". | |
| 190119-02:13:01,528 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref". | |
| 190119-02:13:02,307 nipype.workflow INFO: | |
| [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-02:13:02,611 nipype.workflow INFO: | |
| [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: | |
| 3dTshift -ignore 1 -prefix sub-01_task-rest_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 1.4s /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction/sub-01_task-rest_bold_valid.nii | |
| 190119-02:13:03,142 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref". | |
| 190119-02:13:05,696 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". | |
| 190119-02:13:05,838 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform". | |
| 190119-02:13:05,925 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt". | |
| 190119-02:13:06,324 nipype.workflow INFO: | |
| [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") | |
| 190119-02:13:06,344 nipype.workflow INFO: | |
| [Node] Setting-up "_t1_conform0" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". | |
| 190119-02:13:06,501 nipype.workflow INFO: | |
| [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: | |
| mcflirt -in /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-01_task-rest_bold_valid.nii -out /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-01_task-rest_bold_valid_mcf.nii.gz -reffile /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz -mats -plots | |
| 190119-02:13:06,846 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". | |
| 190119-02:13:07,80 nipype.workflow INFO: | |
| [Node] Running "_t1_conform0" ("fmriprep.interfaces.images.Conform") | |
| 190119-02:13:13,330 nipype.workflow INFO: | |
| [Node] Finished "_t1_conform0". | |
| 190119-02:13:13,525 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform". | |
| 190119-02:13:14,365 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config". | |
| 190119-02:13:14,784 nipype.workflow INFO: | |
| [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs") | |
| 190119-02:13:15,11 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config". | |
| 190119-02:13:27,166 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction". | |
| 190119-02:13:27,921 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform". | |
| 190119-02:13:28,107 nipype.workflow INFO: | |
| [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:13:32,945 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform". | |
| 190119-02:13:33,932 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_split" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_split". | |
| 190119-02:13:34,138 nipype.workflow INFO: | |
| [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: | |
| fslsplit /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform/sub-01_task-rest_bold_valid_tshift_xform.nii.gz -t | |
| 190119-02:14:30,198 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_split". | |
| 190119-02:14:32,698 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/ica_aroma_wf/bold_mni_trans_wf/gen_ref". | |
| 190119-02:14:33,134 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 190119-02:14:33,353 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref". | |
| 190119-02:14:33,643 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 190119-02:14:34,87 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref". | |
| 190119-02:14:34,247 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref". | |
| 190119-02:14:35,981 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". | |
| 190119-02:14:36,175 nipype.workflow INFO: | |
| [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: | |
| antsAI -c [10,0.000001,10] -d 3 -x /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 | |
| 190119-02:14:49,595 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". | |
| 190119-02:14:50,154 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". | |
| 190119-02:14:50,415 nipype.workflow INFO: | |
| [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 | |
| 190119-02:14:55,387 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". | |
| 190119-02:14:56,314 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". | |
| 190119-02:14:56,443 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] | |
| 190119-02:15:01,159 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". | |
| 190119-02:15:02,38 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". | |
| 190119-02:15:02,245 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz | |
| 190119-02:15:03,27 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". | |
| 190119-02:15:04,123 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 190119-02:15:04,405 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip". | |
| 190119-02:15:04,539 nipype.workflow INFO: | |
| [Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command: | |
| antsBrainExtraction.sh -a /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii -m /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/tpl-OASIS30ANTs_res-01_class-brainmask_probtissue.nii.gz -e /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz -d 3 -f /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BrainCerebellumExtraction_roi.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1 | |
| 190119-02:15:21,735 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt". | |
| 190119-02:15:24,865 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". | |
| 190119-02:15:24,981 nipype.workflow INFO: | |
| [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") | |
| 190119-02:15:25,139 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion". | |
| 190119-02:15:26,450 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp". | |
| 190119-02:15:26,502 nipype.workflow INFO: | |
| [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 190119-02:15:26,623 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp". | |
| 190119-02:15:28,43 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". | |
| 190119-02:15:28,127 nipype.workflow INFO: | |
| [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz | |
| 190119-02:15:30,318 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". | |
| 190119-02:15:32,49 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". | |
| 190119-02:15:32,155 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m | |
| 190119-02:15:34,533 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". | |
| 190119-02:15:36,18 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". | |
| 190119-02:15:36,65 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz | |
| 190119-02:15:36,495 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". | |
| 190119-02:15:38,53 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". | |
| 190119-02:15:38,96 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-02:15:38,547 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". | |
| 190119-02:15:40,58 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". | |
| 190119-02:15:40,128 nipype.workflow INFO: | |
| [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: | |
| 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-02:15:42,64 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". | |
| 190119-02:15:44,104 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". | |
| 190119-02:15:44,150 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:15:44,439 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". | |
| 190119-02:15:46,35 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". | |
| 190119-02:15:46,90 nipype.workflow INFO: | |
| [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: | |
| 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz | |
| 190119-02:15:46,834 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". | |
| 190119-02:15:48,55 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". | |
| 190119-02:15:48,89 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-02:15:48,216 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". | |
| 190119-02:15:50,46 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". | |
| 190119-02:15:50,88 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz | |
| 190119-02:15:50,488 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". | |
| 190119-02:15:52,52 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". | |
| 190119-02:15:52,94 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz | |
| 190119-02:15:52,610 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". | |
| 190119-03:31:29,296 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip". | |
| 190119-03:31:40,822 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". | |
| 190119-03:31:42,513 nipype.workflow INFO: | |
| [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK") | |
| 190119-03:34:22,874 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk". | |
| 190119-03:34:25,526 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1". | |
| 190119-03:34:25,801 nipype.workflow INFO: | |
| [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon1 -i /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii -noskullstrip -hires -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer -expert /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts | |
| 190119-13:45:38,968 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1". | |
| 190119-13:45:48,355 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm". | |
| 190119-13:45:48,558 nipype.workflow INFO: | |
| [Node] Running "fsnative_2_t1_xfm" ("fmriprep.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command: | |
| mri_robust_register --satit --iscale --lta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer/sub-01/mri/T1.mgz --dst /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii | |
| 190119-13:45:48,983 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_transform". | |
| 190119-13:45:50,540 nipype.workflow INFO: | |
| [Node] Running "bold_transform" ("fmriprep.interfaces.itk.MultiApplyTransforms") | |
| 190119-13:52:34,378 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform". | |
| 190119-13:52:41,799 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". | |
| 190119-13:52:42,77 nipype.workflow INFO: | |
| [Node] Running "skull_strip_extern" ("fmriprep.interfaces.freesurfer.FSInjectBrainExtracted") | |
| 190119-13:52:42,545 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge". | |
| 190119-13:52:44,138 nipype.workflow INFO: | |
| [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") | |
| 190119-13:53:16,404 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". | |
| 190119-13:54:11,429 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge". | |
| 190119-13:54:12,86 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate". | |
| 190119-13:54:12,333 nipype.workflow INFO: | |
| [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-13:54:18,788 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate". | |
| 190119-13:54:20,78 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". | |
| 190119-13:54:20,248 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 190119-13:54:20,803 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". | |
| 190119-13:54:22,70 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref". | |
| 190119-13:54:22,229 nipype.workflow INFO: | |
| [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage") | |
| 190119-13:54:22,899 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref". | |
| 190119-13:54:24,71 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". | |
| 190119-13:54:24,279 nipype.workflow INFO: | |
| [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: | |
| antsAI -c [10,0.000001,10] -d 3 -x /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 | |
| 190119-13:54:39,216 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". | |
| 190119-13:54:40,155 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". | |
| 190119-13:54:40,327 nipype.workflow INFO: | |
| [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 | |
| 190119-13:54:43,483 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". | |
| 190119-13:54:44,128 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". | |
| 190119-13:54:44,296 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] | |
| 190119-13:54:47,254 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". | |
| 190119-13:54:48,145 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". | |
| 190119-13:54:48,307 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz | |
| 190119-13:54:49,48 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". | |
| 190119-13:54:50,348 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 190119-13:54:50,946 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". | |
| 190119-13:54:51,199 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:54:51,228 nipype.workflow INFO: | |
| [Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:54:51,245 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-01 -sd /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/orwa_4cpus_fmriprep_output/freesurfer | |
| 190119-13:55:11,693 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm". | |
| 190119-13:55:12,175 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". | |
| 190119-13:55:12,343 nipype.workflow INFO: | |
| [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz | |
| 190119-13:55:14,130 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". | |
| 190119-13:55:16,144 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". | |
| 190119-13:55:16,317 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m | |
| 190119-13:55:19,344 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". | |
| 190119-13:55:20,135 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". | |
| 190119-13:55:20,335 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz | |
| 190119-13:55:21,194 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". | |
| 190119-13:55:22,187 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". | |
| 190119-13:55:22,520 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-13:55:23,252 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". | |
| 190119-13:55:24,149 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". | |
| 190119-13:55:24,403 nipype.workflow INFO: | |
| [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: | |
| 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz | |
| 190119-13:55:31,776 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". | |
| 190119-13:55:32,162 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". | |
| 190119-13:55:32,309 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-13:55:32,926 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". | |
| 190119-13:55:34,156 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". | |
| 190119-13:55:34,570 nipype.workflow INFO: | |
| [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: | |
| 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz | |
| 190119-13:55:42,157 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". | |
| 190119-13:55:44,230 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". | |
| 190119-13:55:44,549 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 190119-13:55:45,151 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". | |
| 190119-13:55:46,214 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". | |
| 190119-13:55:46,628 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz | |
| 190119-13:55:47,201 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". | |
| 190119-13:55:48,202 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_confounds_wf/dvars". | |
| 190119-13:55:48,585 nipype.workflow INFO: | |
| [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 190119-13:56:02,351 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars". | |
| 190119-13:56:06,330 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". | |
| 190119-13:56:06,890 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz | |
| 190119-13:56:07,697 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". | |
| 190119-13:56:08,606 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm". | |
| 190119-13:56:08,938 nipype.workflow INFO: | |
| [Node] Running "t1_2_fsnative_xfm" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta | |
| 190119-13:56:09,607 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm". | |
| 190119-13:56:10,548 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk". | |
| 190119-13:56:11,120 nipype.workflow INFO: | |
| [Node] Running "lta_2_itk" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /data/cephfs/punim0752/fmriprep/orwa_1sub_4cpus/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt | |
| 190119-13:56:11,672 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk". | |
| slurmstepd: error: *** JOB 7250036 ON spartan-rc156 CANCELLED AT 2019-01-20T14:11:51 DUE TO TIME LIMIT *** |
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