Hoffman2:Scripts: Difference between revisions
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[[Hoffman2|Back to all things Hoffman2]] | [[Hoffman2|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 | 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. | 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. | ||
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How to clean up after yourself and maintain within your quota space. | How to clean up after yourself and maintain within your quota space. | ||
:[[Hoffman2:Scripts:clean_me.py|clean_me.py]] | :[[Hoffman2:Scripts:clean_me.py|clean_me.py]] | ||
==clear_scratch.sh== | ==clear_scratch.sh== | ||
Clear out all the temporary files you kept in your [[Hoffman2:Introduction#Temporary_Storage|scratch]] directory. | Clear out all the temporary files you kept in your [[Hoffman2:Introduction#Temporary_Storage|scratch]] directory. | ||
:[[Hoffman2:Scripts:clear_scratch.sh|clear_scratch.sh]] | :[[Hoffman2:Scripts:clear_scratch.sh|clear_scratch.sh]] | ||
<!--==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== | ||
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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. | 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. | ||
:[[Hoffman2:Scripts:getDicomDate.py|getDicomDate.py]] | :[[Hoffman2:Scripts:getDicomDate.py|getDicomDate.py]] | ||
<!--==home9_fix.sh== | <!--==home9_fix.sh== | ||
You have a very | You have a very outdated 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]]--> | ||
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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 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. | ||
:[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]] | :[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]] | ||
<!--==mkstruc.sh== | <!--==mkstruc.sh== | ||
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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]] | ||
==switch_fsl== | ==switch_fsl== | ||
Use this one to stay consistent | Use this one to stay consistent with your FSL version. | ||
:[[Hoffman2:Scripts:switch_fsl|switch_fsl]] --> | :[[Hoffman2:Scripts:switch_fsl|switch_fsl]] --> | ||
==setup_subject== | ==setup_subject== | ||
Transfer Dicom data from Dicom server and do NIFTI Convert and other | Transfer Dicom data from the Dicom server and do NIFTI Convert and other processes. | ||
:[[Hoffman2:Scripts:setup_subject|setup_subject]] | :[[Hoffman2:Scripts:setup_subject|setup_subject]] | ||
:[[Hoffman2:Scripts: | :[[Hoffman2:Scripts:setup_subject_3|setup_subject_3]] | ||
==dcmheader.py== | |||
Read, edit Dicom file header information | |||
:[[Hoffman2:Scripts:dcmheader.py|dcmheader.py]] | |||
Latest revision as of 22:54, 5 June 2020
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.
clear_scratch.sh
Clear out all the temporary files you kept in your scratch directory.
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!
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.
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.
setup_subject
Transfer Dicom data from the Dicom server and do NIFTI Convert and other processes.
dcmheader.py
Read, edit Dicom file header information