terminal output from Stella's intro to fmri QC

20130930_stellaIntro_terminalOutput.txt

stowler@pano:/data/birc/Atlanta/PIT/05.Scripts$ bash test_stephen.sh



For each FMRI series: 
  1) counting the number of DICOMs
  2) converting the series into a 4D nifti file:


############### DICOMs from series fMRI_1_6 : ###############
LOCATION  : /data/birc/Atlanta/PIT/origUnzipped/PIT_05_20110803/fMRI_1_6
FILE COUNT: 257
If that's the expected DICOM count for the series, hit 
Enter to continue. (or CTRL-C to quit)
Creating .bxh metafile for series fMRI_1_6...

DcmItem: Length of attribute (230a,4420) is odd
DcmElement: Unknown Tag & Data(230a,4420) larger (1836016489) that remaining bytes in file
Error reading file '/data/birc/Atlanta/PIT/origUnzipped/PIT_05_20110803/fMRI_1_6/00001.dcm.nfo' (may not be DICOM); skipping.
Note: detected wrap-around in slice origins -- assuming 1 images per timepoint.
Added extra dimension: dimnum=4 dimname=t dimsize=256

...done.

Creating nifti volume for series fMRI_1_6...


...done.

Reorienting series fMRI_1_6 nifti volume to match FSL's MNI 152 template...


...done.


############### DICOMs from series fMRI_2_7 : ###############
LOCATION  : /data/birc/Atlanta/PIT/origUnzipped/PIT_05_20110803/fMRI_2_7
FILE COUNT: 257
If that's the expected DICOM count for the series, hit 
Enter to continue. (or CTRL-C to quit)
Creating .bxh metafile for series fMRI_2_7...

DcmItem: Length of attribute (230a,4420) is odd
DcmElement: Unknown Tag & Data(230a,4420) larger (1836016489) that remaining bytes in file
Error reading file '/data/birc/Atlanta/PIT/origUnzipped/PIT_05_20110803/fMRI_2_7/00001.dcm.nfo' (may not be DICOM); skipping.
Note: detected wrap-around in slice origins -- assuming 1 images per timepoint.
Added extra dimension: dimnum=4 dimname=t dimsize=256

...done.

Creating nifti volume for series fMRI_2_7...


...done.

Reorienting series fMRI_2_7 nifti volume to match FSL's MNI 152 template...


...done.

total 266592
-rw-r--r-- 1 stowler centrify    57737 Sep 30 16:53 fmriSeriesfMRI_1_6.bxh
-rw-r--r-- 1 stowler centrify 58796685 Sep 30 16:53 fmriSeriesfMRI_1_6_MNI.nii.gz
-rw-r--r-- 1 stowler centrify 77594976 Sep 30 16:53 fmriSeriesfMRI_1_6.nii
-rw-r--r-- 1 stowler centrify    57738 Sep 30 16:57 fmriSeriesfMRI_2_7.bxh
-rw-r--r-- 1 stowler centrify 58871134 Sep 30 16:58 fmriSeriesfMRI_2_7_MNI.nii.gz
-rw-r--r-- 1 stowler centrify 77594976 Sep 30 16:57 fmriSeriesfMRI_2_7.nii


Now opening fslview to confirm that each reoriented _MNI volume has
orientation consistent with the MNI152 template...

If you are happy with what you seen in fslview, hit 
Enter to continue. (or CTRL-C to quit)

Creating QC report for series fMRI_1_6 fMRI_2_7:

convert: unable to read font `/usr/share/fonts/default/Type1/n019003l.pfb'.
convert: unable to read font `/usr/share/fonts/default/Type1/n019003l.pfb'.
Done!  Output is in /tmp/qcPIT-PIT005-1scr-FmriFingerTapping/qcReport-FBIRN/index.html

...done.

To inspect the QC report just point your web browser at file:///tmp/qcPIT-PIT005-1scr-FmriFingerTapping/qcReport-FBIRN/index.html

If you are happy with the conversion and QC results, copy the output files
from the temporary /tmp/qcPIT-PIT005-1scr-FmriFingerTapping to your project folder. 
Something like:

mkdir -p /data/birc/Atlanta/PIT/06.acqfiles/PIT005/1scr/FmriFingerTapping
mkdir -p /data/birc/Atlanta/PIT/08.QC/PIT005/1scr/FmriFingerTapping
cp /tmp/qcPIT-PIT005-1scr-FmriFingerTapping/*.nii* /data/birc/Atlanta/PIT/06.acqfiles/PIT005/1scr/FmriFingerTapping
cp /tmp/qcPIT-PIT005-1scr-FmriFingerTapping/*.bxh  /data/birc/Atlanta/PIT/06.acqfiles/PIT005/1scr/FmriFingerTapping
cp -r /tmp/qcPIT-PIT005-1scr-FmriFingerTapping/qcReport-FBIRN /data/birc/Atlanta/PIT/08.QC/PIT005/1scr/FmriFingerTapping

...then the last step is for you to delete your temporary directory /tmp/qcPIT-PIT005-1scr-FmriFingerTapping .

268M	/tmp/qcPIT-PIT005-1scr-FmriFingerTapping


stowler@pano:/data/birc/Atlanta/PIT/05.Scripts$ dfgasdgfasdgf