OSGM Script - Revision history

Chris: /* Contrasts */

2022-07-21T17:54:08Z

Contrasts

← Older revision		Revision as of 13:54, 21 July 2022
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	=== Contrasts ===		=== Contrasts ===
	In the analysis directory will be a series of .mat files: one for each contrast you defined using mkcontrast-sess. Your ~~matrix~~ of contrast names should be the names of each of these contrasts you would like to see at the group level -- just omit the .mat part of the filename.		In the analysis directory will be a series of .mat and .config files: one for each contrast you defined using mkcontrast-sess. Your set of contrast names should be the names of each of these contrasts you would like to see at the group level -- just omit the .mat or .config part of the filename.

	[[Category: FreeSurfer]]		[[Category: FreeSurfer]]
	[[Category: Functional Analyses]]		[[Category: Functional Analyses]]

Chris: /* Example Script */

2019-06-04T20:31:53Z

Example Script

← Older revision		Revision as of 16:31, 4 June 2019
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	done		done
	done		done


	#There appears to be no cached file for multiple comparison correction in		#There appears to be no cached file for multiple comparison correction in
	#MNI space, so this loop handles the mni-space analysis		#MNI space, so this loop handles the mni-space analysis

Chris: /* Example Script */

2019-06-04T20:31:41Z

Example Script

← Older revision		Revision as of 16:31, 4 June 2019
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	done		done
	done		done


	#There appears to be no cached file for multiple comparison correction in		#There appears to be no cached file for multiple comparison correction in
	#MNI space, so this loop handles the mni-space analysis		#MNI space, so this loop handles the mni-space analysis

Chris: /* Example Script */

2019-06-04T20:30:51Z

Example Script

← Older revision		Revision as of 16:30, 4 June 2019
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	--surface fsaverage ${hemi} --glmdir glm.wls --nii.gz		--surface fsaverage ${hemi} --glmdir glm.wls --nii.gz
	#correct for multiple comparisons		#correct for multiple comparisons
	mri_glmfit-sim --glmdir glm.wls --cache 2 ~~pos~~ --cwpvalthresh .~~025~~		mri_glmfit-sim --glmdir glm.wls --cache 2 abs --cwpvalthresh .0167
	cd ${ANDIR} #go back to the analysis directory		cd ${ANDIR} #go back to the analysis directory
	done		done
	done		done
	done		done
			#There appears to be no cached file for multiple comparison correction in
			#MNI space, so this loop handles the mni-space analysis
			for anls in "${ANALYSES[@]}"
			do
			#the analysis directory contains each contrast directory
			ANDIR=${SUBJECTS_DIR}/${RFXDIR}/${anls}.mni
			#move to analysis directory for the first time
			cd ${ANDIR}
			for con in "${CONTRASTS[@]}"
			do
			cd ${con}
			mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm \
			--glmdir glm.wls --nii.gz
			#correct for multiple comparisons
			mri_glmfit-sim --glmdir glm.wls --sim perm 1000 2 perm.abs.01 \
			--sim-sign abs --cwp 0.05 --3spaces
			cd ${ANDIR} #go back to the analysis directory
			done
			done

	This script ran mri_glmfit on the fsaverage surface for each hemisphere/surface appearing in the HEMIS array. The output volumes go into the glmdir (in this case a directory called glm.wls) and will be saved as gzipped .nii files. The script also did cluster size thresholding using a cached Monte Carlo simulation with uncorrected .01 ("cache 2", or p=10E-02) p-values for positive t-scores. The thresholding was corrected by dividing .05 by 2, the total number of surfaces examined. A more clever way would be to determine the cwpvalthresh by calling the Unix ''bc'' function to calculate it according to the size of the HEMIS array.		This script ran mri_glmfit on the fsaverage surface for each hemisphere/surface appearing in the HEMIS array. The output volumes go into the glmdir (in this case a directory called glm.wls) and will be saved as gzipped .nii files. The script also did cluster size thresholding using a cached Monte Carlo simulation with uncorrected .01 ("cache 2", or p=10E-02) p-values for positive t-scores. The thresholding was corrected by dividing .05 by 2, the total number of surfaces examined. A more clever way would be to determine the cwpvalthresh by calling the Unix ''bc'' function to calculate it according to the size of the HEMIS array.

192.168.1.1 at 17:36, 28 September 2017

2017-09-28T17:36:54Z

← Older revision		Revision as of 13:36, 28 September 2017
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	[[Category: FreeSurfer]]		[[Category: FreeSurfer]]
			[[Category: Functional Analyses]]

192.168.1.1: /* What values do I use for ANALYSES and CONTRASTS? */

2017-09-28T17:32:06Z

What values do I use for ANALYSES and CONTRASTS?

← Older revision		Revision as of 13:32, 28 September 2017
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	=== Contrasts ===		=== Contrasts ===
	In the analysis directory will be a series of .mat files: one for each contrast you defined using mkcontrast-sess. Your matrix of contrast names should be the names of each of these contrasts you would like to see at the group level -- just omit the .mat part of the filename.		In the analysis directory will be a series of .mat files: one for each contrast you defined using mkcontrast-sess. Your matrix of contrast names should be the names of each of these contrasts you would like to see at the group level -- just omit the .mat part of the filename.

			[[Category: FreeSurfer]]

192.168.1.1: /* Example Script */

2017-09-28T17:27:48Z

Example Script

← Older revision		Revision as of 13:27, 28 September 2017
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	SUBJECTS_DIR=`pwd`		SUBJECTS_DIR=`pwd`
	RFXDIR=RFX #This is the name of the directory into which the group-level analyses will go		RFXDIR=RFX #This is the name of the directory into which the group-level analyses will go
	HEMIS=( lh rh ) #Which hemispheres are you analyzing? Possible choices are [lh \| rh \| mni305]		HEMIS=( <span style="color:red">lh</span> <span style="color:blue">rh</span> ) #Which hemispheres are you analyzing? Possible choices are [lh \| rh \| mni305]
	ANALYSES=( LDT.fsaverage.sm4.down ) #Name of the analysis directory created by mkanalysis-sess		ANALYSES=( LDT.fsaverage.sm4.down ) #Name of the analysis directory created by mkanalysis-sess
	CONTRASTS=( <span style="color:red">task</span> w-v-pw hi-v-lo ) #Names of all contrasts you're interested in		CONTRASTS=( <span style="color:red">task</span> <span style="color:green">w-v-pw</span> <span style="color:blue">hi-v-lo</span> ) #Names of all contrasts you're interested in

	for hemi in "${HEMIS[@]}"		for hemi in "${HEMIS[@]}"

192.168.1.1: /* Example Script */

2017-09-28T17:26:40Z

Example Script

← Older revision		Revision as of 13:26, 28 September 2017
Line 9:		Line 9:
	HEMIS=( lh rh ) #Which hemispheres are you analyzing? Possible choices are [lh \| rh \| mni305]		HEMIS=( lh rh ) #Which hemispheres are you analyzing? Possible choices are [lh \| rh \| mni305]
	ANALYSES=( LDT.fsaverage.sm4.down ) #Name of the analysis directory created by mkanalysis-sess		ANALYSES=( LDT.fsaverage.sm4.down ) #Name of the analysis directory created by mkanalysis-sess
	CONTRASTS=( task w-v-pw hi-v-lo ) #Names of all contrasts you're interested in		CONTRASTS=( <span style="color:red">task</span> w-v-pw hi-v-lo ) #Names of all contrasts you're interested in

	for hemi in "${HEMIS[@]}"		for hemi in "${HEMIS[@]}"

192.168.1.1: /* Example Script */

2017-09-28T17:25:41Z

Example Script

← Older revision		Revision as of 13:25, 28 September 2017
Line 31:		Line 31:
	done		done
	done		done

			This script ran mri_glmfit on the fsaverage surface for each hemisphere/surface appearing in the HEMIS array. The output volumes go into the glmdir (in this case a directory called glm.wls) and will be saved as gzipped .nii files. The script also did cluster size thresholding using a cached Monte Carlo simulation with uncorrected .01 ("cache 2", or p=10E-02) p-values for positive t-scores. The thresholding was corrected by dividing .05 by 2, the total number of surfaces examined. A more clever way would be to determine the cwpvalthresh by calling the Unix ''bc'' function to calculate it according to the size of the HEMIS array.

	== What values do I use for ANALYSES and CONTRASTS? ==		== What values do I use for ANALYSES and CONTRASTS? ==

192.168.1.1: Created page with "A BASH script can be written to take the tedium out of running group level analyses for multiple contrasts. ==Example Script== Below is a script I wrote to run mri_glmfit and..."

2017-09-28T17:20:17Z

Created page with "A BASH script can be written to take the tedium out of running group level analyses for multiple contrasts. ==Example Script== Below is a script I wrote to run mri_glmfit and..."

New page

A BASH script can be written to take the tedium out of running group level analyses for multiple contrasts.

==Example Script==
Below is a script I wrote to run mri_glmfit and mri_glmfit-sim on a set of 3 contrasts. It accomplishes this by executing the commands within a nested loop.

#!/bin/bash
SUBJECTS_DIR=`pwd`
RFXDIR=RFX #This is the name of the directory into which the group-level analyses will go
HEMIS=( lh rh ) #Which hemispheres are you analyzing? Possible choices are [lh | rh | mni305]
ANALYSES=( LDT.fsaverage.sm4.down ) #Name of the analysis directory created by mkanalysis-sess
CONTRASTS=( task w-v-pw hi-v-lo ) #Names of all contrasts you're interested in

for hemi in "${HEMIS[@]}"
do
for anls in "${ANALYSES[@]}"
do
#the analysis directory contains each contrast directory
ANDIR=${SUBJECTS_DIR}/${RFXDIR}/${anls}.${hemi}
#move to analysis directory for the first time
cd ${ANDIR}
for con in "${CONTRASTS[@]}"
do
cd ${con}
pwd
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm \
--surface fsaverage ${hemi} --glmdir glm.wls --nii.gz
#correct for multiple comparisons
mri_glmfit-sim --glmdir glm.wls --cache 2 pos --cwpvalthresh .025
cd ${ANDIR} #go back to the analysis directory
done
done
done

== What values do I use for ANALYSES and CONTRASTS? ==
The above script runs in nested for-loops that iterate through each entry in the ANALYSES and CONTRASTS arrays. The script comments tell you what these array values represent, but you might not be clear what the correct values should be.

=== Analyses ===
When you ran mkanalysis-sess in your <code>SUBJECTS_DIR</code>, 1, 2 or 3 directories were created, and will be sitting along-side your individual participant directories. These will have names like ''my_analysis.lh'', ''my_analysis.rh'', and ''my_analysis.mni305''. In this case, your ANALYSES array declaration should read like:
ANALYSES=( my_analysis )
Where you omit the part of the directory name that indicates the surface/space (lh/rh/mni305).
It is our usual practice to use analysis folder names that give some indication of the nature of the processing that was done, and the surface that was used (self or fsaverage). In the above script, the analysis folder is called ''LDT.fsaverage.sm4.down'' because it used par-files called LDT, used the fsaverage surface for the first-level analysis, and the data used a 4mm smoothing kernel and were slice-time corrected in the down direction.

=== Contrasts ===
In the analysis directory will be a series of .mat files: one for each contrast you defined using mkcontrast-sess. Your matrix of contrast names should be the names of each of these contrasts you would like to see at the group level -- just omit the .mat part of the filename.