Hoffman2:Scripts - Revision history

Hwang at 22:15, 19 May 2025

2025-05-19T22:15:01Z

← Older revision		Revision as of 22:15, 19 May 2025
Line 5:		Line 5:
	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.


			==clean_up.sh==
			Clean up files such as tsplot and FSL stderr
			:[[Hoffman2:Scripts:clean_up.sh\|clean_up.sh]]

	==clean_me.py==		==clean_me.py==

Hwang at 22:01, 14 August 2024

2024-08-14T22:01:53Z

← Older revision		Revision as of 22:01, 14 August 2024
Line 59:		Line 59:
	Read, edit Dicom file header information		Read, edit Dicom file header information
	:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]		:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]

			==gen_movie.py==
			Convert MRI file into a movie
			:[[Hoffman2:Scripts:gen_movie.py\|gen_movie.py]]

Jpdiaz: minor format edits

2020-06-05T22:54:32Z

minor format edits

← Older revision		Revision as of 22:54, 5 June 2020
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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, because let's face it, history has a way of repeating itself.		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 ~~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 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 on your FSL version.		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 ~~process~~.		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:setup_subject_3\|setup_subject_3]]		:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]

Hwang: /* dcmheader.py */

2020-04-27T22:18:09Z

dcmheader.py

← Older revision		Revision as of 22:18, 27 April 2020
Line 65:		Line 65:
	Read, edit Dicom file header information		Read, edit Dicom file header information
	:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]		:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]

	~~===Purpose:===~~

	~~This script is to help view and edit a Dicom file header information or header of Dicom files under the same subject folder~~

	~~===Usage:===~~
	~~To use this script, you need to load python module first and export the library location:~~

	~~module load python/3.6.1_shared~~
	~~PYTHONPATH=/u/project/CCN/apps/python_libs/3.6/site-packages/~~

	~~Then run the code as~~

	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -h~~

	~~This will show you the code usage.~~

	~~This code can show the header of a single dcm file, or shows specific header items in multiple files inside the same subject folder or update them.~~

	~~For example, showing the full header of a dcm file~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/file -p (or --print )~~

	~~You want to use this first to find out the tags of the header items you want to check or update. For example you will get the following result~~

	~~(0010, 0010) Patient's Name PN: '12345'~~
	~~(0010, 0020) Patient ID LO: 12345~~
	~~(0010, 0030) Patient's Birth Date DA: '20000101'~~
	~~(0010, 0040) Patient's Sex CS: 'F'~~
	~~(0010, 1010) Patient's Age AS: '020Y'~~

	~~(0010, 0010) is the tag for item “Patient's Name”, you need this for -c (--check) and -u (--update) options.~~

	~~-c (--check) option:~~
	~~This option is to view specific header items in a dcm file or the same items in all files inside the subject folder~~

	~~View a single item:~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -c "(0010, 0010)"~~

	~~View a single item in a subject folder by specifying the folder instead of a file:~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -c "(0010, 0010)"~~

	~~View multiple items:~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -c "(0010, 0010) (0010, 0020)"~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -c "(0010, 0010) (0010, 0020)"~~

	~~-u (--update) option:~~
	~~This option is for updating specific header items, using the format as "tag=new_value"~~
	~~Example:~~
	~~update a single item (in this example, change the Patient's Name value to 12345_1):~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -u "(0010, 0010)=12345_1"~~
	~~update the same item for the whole subject folder~~
	~~python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -u "(0010, 0010)=12345_1"~~

Hwang: /* dcmheader.py */

2020-04-27T22:16:25Z

dcmheader.py

← Older revision		Revision as of 22:16, 27 April 2020
Line 65:		Line 65:
	Read, edit Dicom file header information		Read, edit Dicom file header information
	:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]		:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]

			===Purpose:===

			This script is to help view and edit a Dicom file header information or header of Dicom files under the same subject folder

			===Usage:===
			To use this script, you need to load python module first and export the library location:

			module load python/3.6.1_shared
			PYTHONPATH=/u/project/CCN/apps/python_libs/3.6/site-packages/

			Then run the code as

			python3 /u/project/CCN/apps/scripts/dcmheader.py -h

			This will show you the code usage.

			This code can show the header of a single dcm file, or shows specific header items in multiple files inside the same subject folder or update them.

			For example, showing the full header of a dcm file
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/file -p (or --print )

			You want to use this first to find out the tags of the header items you want to check or update. For example you will get the following result

			(0010, 0010) Patient's Name PN: '12345'
			(0010, 0020) Patient ID LO: 12345
			(0010, 0030) Patient's Birth Date DA: '20000101'
			(0010, 0040) Patient's Sex CS: 'F'
			(0010, 1010) Patient's Age AS: '020Y'

			(0010, 0010) is the tag for item “Patient's Name”, you need this for -c (--check) and -u (--update) options.

			-c (--check) option:
			This option is to view specific header items in a dcm file or the same items in all files inside the subject folder

			View a single item:
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -c "(0010, 0010)"

			View a single item in a subject folder by specifying the folder instead of a file:
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -c "(0010, 0010)"

			View multiple items:
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -c "(0010, 0010) (0010, 0020)"
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -c "(0010, 0010) (0010, 0020)"

			-u (--update) option:
			This option is for updating specific header items, using the format as "tag=new_value"
			Example:
			update a single item (in this example, change the Patient's Name value to 12345_1):
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/file -u "(0010, 0010)=12345_1"
			update the same item for the whole subject folder
			python3 /u/project/CCN/apps/scripts/dcmheader.py -f /path/to/my/dicom/subject/ -u "(0010, 0010)=12345_1"

Hwang: /* dcmheader.py */

2020-04-27T22:12:52Z

dcmheader.py

← Older revision		Revision as of 22:12, 27 April 2020
Line 64:		Line 64:
	==dcmheader.py==		==dcmheader.py==
	Read, edit Dicom file header information		Read, edit Dicom file header information
	:[[Hoffman2:Scripts:dcmheader.py\|dcmheader]]		:[[Hoffman2:Scripts:dcmheader.py\|dcmheader.py]]

Hwang: /* dcmheader */

2020-04-27T22:12:25Z

dcmheader

← Older revision		Revision as of 22:12, 27 April 2020
Line 62:		Line 62:
	:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]		:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]

	==dcmheader==		==dcmheader.py==
	Read, edit Dicom file header information		Read, edit Dicom file header information
	:[[Hoffman2:Scripts:dcmheader\|dcmheader]]		:[[Hoffman2:Scripts:dcmheader.py\|dcmheader]]

Hwang at 22:12, 27 April 2020

2020-04-27T22:12:02Z

← Older revision		Revision as of 22:12, 27 April 2020
Line 61:		Line 61:
	:[[Hoffman2:Scripts:setup_subject\|setup_subject]]		:[[Hoffman2:Scripts:setup_subject\|setup_subject]]
	:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]		:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]

			==dcmheader==
			Read, edit Dicom file header information
			:[[Hoffman2:Scripts:dcmheader\|dcmheader]]

Hwang: /* setup_subject */

2019-10-15T23:19:08Z

setup_subject

← Older revision		Revision as of 23:19, 15 October 2019
Line 60:		Line 60:
	Transfer Dicom data from Dicom server and do NIFTI Convert and other process.		Transfer Dicom data from Dicom server and do NIFTI Convert and other process.
	:[[Hoffman2:Scripts:setup_subject\|setup_subject]]		:[[Hoffman2:Scripts:setup_subject\|setup_subject]]
	:[[Hoffman2:Scripts:~~setup_subject~~\|setup_subject_3]]		:[[Hoffman2:Scripts:setup_subject_3\|setup_subject_3]]

Hwang: /* setup_subject */

2019-10-15T23:18:05Z

setup_subject

← Older revision		Revision as of 23:18, 15 October 2019
Line 60:		Line 60:
	Transfer Dicom data from Dicom server and do NIFTI Convert and other process.		Transfer Dicom data from Dicom server and do NIFTI Convert and other process.
	:[[Hoffman2:Scripts:setup_subject\|setup_subject]]		:[[Hoffman2:Scripts:setup_subject\|setup_subject]]
			:[[Hoffman2:Scripts:setup_subject\|setup_subject_3]]