Hoffman2:Scripts:setup subject - Revision history

Hwang at 16:44, 3 July 2019

2019-07-03T16:44:06Z

Hwang: /* Options: */

2019-06-20T22:27:24Z

Options:

← Older revision		Revision as of 22:27, 20 June 2019
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	mprage : process anatomical scans		mprage : process anatomical scans
	sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command		sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command




	Set SPM compatability		Set SPM compatability

Hwang: /* Options: */

2019-06-20T22:26:59Z

Options:

← Older revision		Revision as of 22:26, 20 June 2019
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	mprage : process anatomical scans		mprage : process anatomical scans
	sge: submit the job in batch mode		sge: submit the job in batch mode

			(Using option diags requires mcflirt, bet and melodic to be processed first)

	-s (or --skip) this option to specify the processing you want to skip		-s (or --skip) this option to specify the processing you want to skip
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	~~(Using option diags requires mcflirt, bet and melodic to be processed first)~~

Hwang: /* Options: */

2019-06-20T22:26:09Z

Options:

← Older revision		Revision as of 22:26, 20 June 2019
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	diags : run diagnostics		diags : run diagnostics
	mprage : process anatomical scans		mprage : process anatomical scans
	sge: submit in batch mode		sge: submit the job in batch mode

	-s (or --skip) this option to specify the processing you want to skip		-s (or --skip) this option to specify the processing you want to skip

Hwang: /* Options: */

2019-06-20T22:24:59Z

Options:

← Older revision		Revision as of 22:24, 20 June 2019
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	diags : run diagnostics		diags : run diagnostics
	mprage : process anatomical scans		mprage : process anatomical scans
	sge: not using batch mode, which means you need to start interactive mode first		sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command

Hwang: /* Examples: */

2019-06-20T22:24:20Z

Examples:

← Older revision		Revision as of 22:24, 20 June 2019
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	setup_subject2 -d mcflirt,bet,melodic,diags,mprage basedir subjectID		setup_subject2 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
	setup_subject2 -d mprage basedir subjectID		setup_subject2 -d mprage basedir subjectID

			Skip mcflirt,bet,melodic,diags
			setup_subject2 -s mcflirt,bet,melodic,diags basedir subjectID

	===Notes===		===Notes===

Hwang: /* Options: */

2019-06-20T22:23:19Z

Options:

← Older revision		Revision as of 22:23, 20 June 2019
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	-s (or --skip) this option to specify the processing you want to skip		-s (or --skip) this option to specify the processing you want to skip
			mcflirt : run mcflirt
			bet : run bet
			melodic : run melodic
			diags : run diagnostics
			mprage : process anatomical scans
			sge: not using batch mode, which means you need to start interactive mode first

Hwang at 22:22, 20 June 2019

2019-06-20T22:22:26Z

← Older revision		Revision as of 22:22, 20 June 2019
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	After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.		After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
	-d (or --do)		-d (or --do) : this option to specify the processing you want to add
	mcflirt : run mcflirt		mcflirt : run mcflirt
	bet : run bet		bet : run bet
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	diags : run diagnostics		diags : run diagnostics
	mprage : process anatomical scans		mprage : process anatomical scans
			sge: submit in batch mode

			-s (or --skip) this option to specify the processing you want to skip


	(Using option diags requires mcflirt, bet and melodic to be processed first)		(Using option diags requires mcflirt, bet and melodic to be processed first)


	Set SPM compatability		Set SPM compatability

Hwang: /* Notes */

2019-05-10T21:37:33Z

Notes

← Older revision		Revision as of 21:37, 10 May 2019
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	===Notes===		===Notes===
	Log File: provides useful details about what commands were run, their output and the script's status It's located at		Log File: provides useful details about what commands were run, their output and the script's status. It's located at

	basedir/subjectID/notes/setup_log.date_numbers		basedir/subjectID/notes/setup_log.date_numbers

Hwang: /* Notes */

2019-05-10T21:30:56Z

Notes

← Older revision		Revision as of 21:30, 10 May 2019
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	===Notes===		===Notes===
	Log File: ~~The log file~~ provides details about what commands were run, their output and the script's status It's located at		Log File: provides useful details about what commands were run, their output and the script's status It's located at

	basedir/subjectID/notes/setup_log.date_numbers		basedir/subjectID/notes/setup_log.date_numbers

← Older revision		Revision as of 16:44, 3 July 2019
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	==Setup_subject script usage==		==Setup_subject script usage==
	~~Setup_subject2~~ (replaced setup_subject) is used to download data from Dicom server and run NIFTI convert on the subject data.		Setup_subject_2 (replaced setup_subject) is used to download data from Dicom server and run NIFTI convert on the subject data.
	Other options such as mcflirt, bet, melodic, diags or mprage can be specified to run FSL processing and others.		Other options such as mcflirt, bet, melodic, diags or mprage can be specified to run FSL processing and others.


	===Basic Usage:===		===Basic Usage:===
	~~setup_subject2~~ [option] basedir subjectID		setup_subject_2 [option] basedir subjectID

	basedir is where you want the processed data to be stored in your Hoffman account,		basedir is where you want the processed data to be stored in your Hoffman account,
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	Download data and run NIFTI convert		Download data and run NIFTI convert
	~~setup_subject2~~ --download ccn,dicomuserid,/dicom/data/YOURGROUP/ basedir subjectID		setup_subject_2 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ basedir subjectID
	( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server user account)		( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server user account)

	Download data and run NIFTI convert and other FSL processing:		Download data and run NIFTI convert and other FSL processing:
	~~setup_subject2~~ --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID		setup_subject_2 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

	Process data only without download		Process data only without download
	~~setup_subject2~~ -d mcflirt,bet,melodic,diags basedir subjectID		setup_subject_2 -d mcflirt,bet,melodic,diags basedir subjectID
	~~setup_subject2~~ -d mcflirt,bet,melodic,diags,mprage basedir subjectID		setup_subject_2 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
	~~setup_subject2~~ -d mprage basedir subjectID		setup_subject_2 -d mprage basedir subjectID

	Skip mcflirt,bet,melodic,diags		Skip mcflirt,bet,melodic,diags
	~~setup_subject2~~ -s mcflirt,bet,melodic,diags basedir subjectID		setup_subject_2 -s mcflirt,bet,melodic,diags basedir subjectID

	===Notes===		===Notes===