Hoffman2:Scripts: Difference between revisions

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==compUsage.py==
<!--==compUsage.py==
Check out how much the FMRI group has been using the cluster.  Useful to know if your job has a snow ball's chance of running before next quarter, or if Wesley's been breaking Hoffman2 again.
Check out how much the FMRI group has been using the cluster.  Useful to know if your job has a snow ball's chance of running before next quarter, or if Wesley's been breaking Hoffman2 again.
:[[Hoffman2:Scripts:compUsage.py|compUsage.py]]
:[[Hoffman2:Scripts:compUsage.py|compUsage.py]]-->




==fix_all_home9.sh==
<!--==fix_all_home9.sh==
A long time ago, the Hoffman2 filesystem had a directory called home9 that many people made use of.  Now that it's gone, some of your scripts point to places that no longer exist.  This tries to fix those scripts.
A long time ago, the Hoffman2 filesystem had a directory called home9 that many people made use of.  Now that it's gone, some of your scripts point to places that no longer exist.  This tries to fix those scripts.
:[[Hoffman2:Scripts:fix_all_home9.sh|fix_all_home9.sh]]
:[[Hoffman2:Scripts:fix_all_home9.sh|fix_all_home9.sh]]-->
 


==fix_perms.sh==
==fix_perms.sh==
Collaboration is one of the best ways to further science.  So if your lab mate can't work on the data you just processed for her, science has a hard time moving forward.  Fix those permissions and collaborate!
Collaboration is one of the best ways to further science.  So if your labmate can't work on the data you just processed for her, science has a hard time moving forward.  Fix those permissions and collaborate!
:[[Hoffman2:Scripts:fix_perms.sh|fix_perms.sh]]
:[[Hoffman2:Scripts:fix_perms.sh|fix_perms.sh]]


==getDicomDate.py==
==getDicomDate.py==
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==home9_fix.sh==
<!--==home9_fix.sh==
You have a very out dated bash profile that refers to the old home9 directory.  Run this script once and all things will be fixed.
You have a very out dated bash profile that refers to the old home9 directory.  Run this script once and all things will be fixed.
:[[Hoffman2:Scripts:home9_fix.sh|home9_fix.sh]]
:[[Hoffman2:Scripts:home9_fix.sh|home9_fix.sh]]-->
 


==matlab_license_check.sh==
==matlab_license_check.sh==
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==mkstruc.sh==
<!--==mkstruc.sh==
Standards are important for uniform understanding. Use our standard data directory tree for your next study.
Standards are important for uniform understanding. Use our standard data directory tree for your next study.
:[[Hoffman2:Scripts:mkstruc.sh|mkstruc.sh]]
:[[Hoffman2:Scripts:mkstruc.sh|mkstruc.sh]]-->
 


==switch_freesurfer==
<!--DMM -->
<!--  ==switch_freesurfer==
Version consistency is important for software.  Use this to stay consistent on the version of FreeSurfer you are using.
Version consistency is important for software.  Use this to stay consistent on the version of FreeSurfer you are using.
:[[Hoffman2:Scripts:switch_freesurfer|switch_freesurfer]]
:[[Hoffman2:Scripts:switch_freesurfer|switch_freesurfer]]
Line 58: Line 55:
==switch_fsl==
==switch_fsl==
Use this one to stay consistent on your FSL version.
Use this one to stay consistent on your FSL version.
:[[Hoffman2:Scripts:switch_fsl|switch_fsl]]
:[[Hoffman2:Scripts:switch_fsl|switch_fsl]] -->
 
==setup_subject==
Transfer Dicom data from Dicom server and do NIFTI Convert and other process.
:[[Hoffman2:Scripts:setup_subject|setup_subject]]
:[[Hoffman2:Scripts:setup_subject_3|setup_subject_3]]
 
==dcmheader.py==
Read, edit Dicom file header information
:[[Hoffman2:Scripts:dcmheader.py|dcmheader.py]]

Revision as of 22:18, 27 April 2020

Back to all things Hoffman2

When you encounter a computer problem, it is best to find a systematic solution in the form of a script or program. This lets you be prepared to handle the problem the next time you encounter it, because let's face it, history has a way of repeating itself.

Here-in lies a collection of the scripts we have built up in the Hoffman2 FMRI group for solving our most common problems. Each script's help output is provided for searching convenience as well as example usage cases for each script.


clean_me.py

How to clean up after yourself and maintain within your quota space.

clean_me.py


clear_scratch.sh

Clear out all the temporary files you kept in your scratch directory.

clear_scratch.sh



fix_perms.sh

Collaboration is one of the best ways to further science. So if your labmate can't work on the data you just processed for her, science has a hard time moving forward. Fix those permissions and collaborate!

fix_perms.sh

getDicomDate.py

All you want to know if when the DICOM got created and you don't have time to learn how to read DICOM files byte-wise. Just run this script.

getDicomDate.py


matlab_license_check.sh

MATLAB Licenses are as valuable as gold at times of heavy computing on Hoffman2. Use this script to find out if there is one with your name on it, or to find out who to go yell at for using too many licenses.

matlab_license_check.sh



setup_subject

Transfer Dicom data from Dicom server and do NIFTI Convert and other process.

setup_subject
setup_subject_3

dcmheader.py

Read, edit Dicom file header information

dcmheader.py