danjgale

danjgale

import os
import natsort
import glob

def get_files(pattern, force_list=False):
    """Extracts files in alphanumerical order that match the provided glob 
    pattern.

    Parameters
    ----------

danjgale

from nilearn.decoding import Searchlight
from nilearn.datasets import load_mni152_brain_mask
from nilearn.image import new_img_like 
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from skearn.svm import LinearSVC
from sklearn.model_selection import LeaveOneGroupOut

imgs = # 4D NIfTI image or list of 3D NIfTI images
y = # array-like of condition labels for each volume in `imgs` 

danjgale

Node: _autorecon30
Working directory: /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30

Node inputs:

FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>

danjgale

RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.06.1-ce -v /Raid6/users/dan/Documents/licenses/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /Raid6/raw/midnight_scan_club:/data:ro -v /Raid6/raw/users/dan/Documents/Projects/midnight_test/data:/out -v /Raid6/users/dan/Documents/Projects/midnight_test/fmriprep_working_dir:/scratch poldracklab/fmriprep:1.2.6-1 /data /out participant --participant-label MSC01 --anat-only -w /scratch
WARNING: Error loading config file: /Raid6/users/dan/.docker/config.json: stat /Raid6/users/dan/.docker/config.json: permission denied
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
This dataset appears to be BIDS compatible.
        Summary:                    Available Tasks:        Available Modalities: 
        7717 Files, 108.71GB        glasslexical            bold                  
        10 - Subjects               memoryscenes            T1w                   
        14 - Sessions               memorywords       

danjgale

Installing Pysurfer with Python 3.6

Pysurfer can be a bit tough to install because the dependencies (e.g., Mayavi) can be tricky to get right. Further, the documentation, at the time of this writing, states that Pysurfer only works with Python 2.7. This is not entirely the case, as Pysurfer does in fact work with Python 3. Here, I've documented the installation steps to get Pysurfer working with Python 3 on OSX (I'm guessing these steps also hold for Linux; not sure about Windows).

Setup

Before we begin, you'll need conda installed to create a virtual environment, and you will also need Freesurfer installed on your computer (follow the installation steps for your operating system, as is, here).

Then, let's set up our conda environment. We'll want to specify Python 3.6 and install some dependencies:

danjgale