Configure mkanalysis-sess - Revision history

Chris at 14:37, 7 October 2020

2020-10-07T14:37:45Z

← Older revision		Revision as of 10:37, 7 October 2020
Line 1:		Line 1:
	The first step in the first-level analysis is to configure analyses and contrasts. This step describes what preprocessing stages should have been run as well as the parameters needed to construct a design matrix (no data are analyzed yet). This is done with mkanalysis-sess.		The first step in the first-level analysis is to configure analyses and contrasts. This step describes what preprocessing stages should have been run as well as the parameters needed to construct a design matrix (no data are analyzed yet). This is done with mkanalysis-sess. You only have to do this one time for your project, and not for each subject in your experiment.

	A good way to make it clear how you are configuring your analysis is to declare important parameters as shell environment variables, and then use them when calling mkanalysis-sess:		A good way to make it clear how you are configuring your analysis is to declare important parameters as shell environment variables, and then use them when calling mkanalysis-sess:

Chris at 17:45, 6 July 2020

2020-07-06T17:45:33Z

← Older revision		Revision as of 13:45, 6 July 2020
Line 6:		Line 6:
	REFEVENTDUR=0.8; #How long are the events?		REFEVENTDUR=0.8; #How long are the events?
	TR=2.047; #What is the TR		TR=2.047; #What is the TR
			[https://en.wikibooks.org/wiki/Neuroimaging_Data_Processing/Temporal_Filtering HIPASS]=0.008 #Hz .008 = 125 seconds
	STC=up; #what is the slice time correction? (up, down, siemens)		STC=up; #what is the slice time correction? (up, down, siemens)
	NCONDITIONS=3; #How many conditions in the par files		NCONDITIONS=3; #How many conditions in the par files
Line 25:		Line 26:
	-nconditions ${NCONDITIONS} \		-nconditions ${NCONDITIONS} \
	-timewindow 24 \		-timewindow 24 \
			-hpf ${HIPASS} \
	-spmhrf 2 \		-spmhrf 2 \
	-polyfit 2 \		-polyfit 2 \

Chris at 01:27, 23 May 2020

2020-05-23T01:27:23Z

← Older revision		Revision as of 21:27, 22 May 2020
Line 20:		Line 20:
	-surface ${SURFACE} ${hemi} \		-surface ${SURFACE} ${hemi} \
	-fwhm ${SMOOTHING} \		-fwhm ${SMOOTHING} \
	-stc ${STC}		-stc ${STC} \
	-event-related \		-event-related \
	-paradigm ${PARFILE} \		-paradigm ${PARFILE} \
Line 37:		Line 37:
	-fsd bold \		-fsd bold \
	-mni305 2 \		-mni305 2 \
			-stc ${STC} \
	-fwhm ${SMOOTHING} \		-fwhm ${SMOOTHING} \
	-event-related \		-event-related \

Chris at 01:26, 23 May 2020

2020-05-23T01:26:04Z

← Older revision		Revision as of 21:26, 22 May 2020
Line 6:		Line 6:
	REFEVENTDUR=0.8; #How long are the events?		REFEVENTDUR=0.8; #How long are the events?
	TR=2.047; #What is the TR		TR=2.047; #What is the TR
			STC=up; #what is the slice time correction? (up, down, siemens)
	NCONDITIONS=3; #How many conditions in the par files		NCONDITIONS=3; #How many conditions in the par files
	SURFACE=fsaverage; #generally valid options are 'self' or 'fsaverage'		SURFACE=fsaverage; #generally valid options are 'self' or 'fsaverage'
Line 11:		Line 12:
	PARFILE=FAM.par; #What's the name of the .par files in your bold/ directories?		PARFILE=FAM.par; #What's the name of the .par files in your bold/ directories?
	ANROOT="FAM.sm" #base name for the analysis directories		ANROOT="FAM.sm" #base name for the analysis directories


	for hemi in "${HEMIS[@]}"		for hemi in "${HEMIS[@]}"
Line 18:		Line 20:
	-surface ${SURFACE} ${hemi} \		-surface ${SURFACE} ${hemi} \
	-fwhm ${SMOOTHING} \		-fwhm ${SMOOTHING} \
			-stc ${STC}
	-event-related \		-event-related \
	-paradigm ${PARFILE} \		-paradigm ${PARFILE} \

Chris at 18:42, 30 May 2019

2019-05-30T18:42:14Z

@@ Line 30: / Line 30: @@
    -per-run -force
   done
 The above code could be saved as a script in your ~/bin directory (e.g., mkanalysis.sh) and modified as required for different datasets or parametric choices.

Chris at 22:04, 28 February 2019

2019-02-28T22:04:58Z

← Older revision		Revision as of 18:04, 28 February 2019
Line 35:		Line 35:

	Note that there is also a directive to skip volumes, however it doesn't seem to do what we expect it to, and so we just drop those volumes from the data entirely, and modify the event onsets to account for the dropped volumes.		Note that there is also a directive to skip volumes, however it doesn't seem to do what we expect it to, and so we just drop those volumes from the data entirely, and modify the event onsets to account for the dropped volumes.

			[[Category:FreeSurfer]]

Chris at 22:02, 28 February 2019

2019-02-28T22:02:56Z

← Older revision		Revision as of 18:02, 28 February 2019
Line 9:		Line 9:
	SURFACE=fsaverage; #generally valid options are 'self' or 'fsaverage'		SURFACE=fsaverage; #generally valid options are 'self' or 'fsaverage'
	HEMIS=( lh rh ); #for automatically looping over both hemispheres		HEMIS=( lh rh ); #for automatically looping over both hemispheres
	PARFILE=~~LDT~~.par; #What's the name of the .par files in your bold/ directories?		PARFILE=FAM.par; #What's the name of the .par files in your bold/ directories?
	ANROOT="~~LDT~~.sm" #base name for the analysis directories		ANROOT="FAM.sm" #base name for the analysis directories

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

Erica at 14:57, 19 June 2018

2018-06-19T14:57:03Z

← Older revision		Revision as of 10:57, 19 June 2018
Line 32:		Line 32:
	The above code could be saved as a script in your ~/bin directory (e.g., mkanalysis.sh) and modified as required for different datasets or parametric choices.		The above code could be saved as a script in your ~/bin directory (e.g., mkanalysis.sh) and modified as required for different datasets or parametric choices.

	This step creates analysis directories in your $SUBJECTS_DIR containing single files that contain all the information needed for the next step.		This step creates analysis directories in your $SUBJECTS_DIR containing single files that contain all the information needed for the next step. Your $SUBJECTS_DIR should be your project root directory.

	Note that there is also a directive to skip volumes, however it doesn't seem to do what we expect it to, and so we just drop those volumes from the data entirely, and modify the event onsets to account for the dropped volumes.		Note that there is also a directive to skip volumes, however it doesn't seem to do what we expect it to, and so we just drop those volumes from the data entirely, and modify the event onsets to account for the dropped volumes.

128.205.173.88 at 15:50, 18 January 2018

2018-01-18T15:50:31Z

← Older revision		Revision as of 11:50, 18 January 2018
Line 7:		Line 7:
	TR=2.047; #What is the TR		TR=2.047; #What is the TR
	NCONDITIONS=3; #How many conditions in the par files		NCONDITIONS=3; #How many conditions in the par files
	SURFACE=~~self~~; #generally valid options are 'self' or 'fsaverage'		SURFACE=fsaverage; #generally valid options are 'self' or 'fsaverage'
	HEMIS=( lh rh ); #for automatically looping over both hemispheres		HEMIS=( lh rh ); #for automatically looping over both hemispheres
	PARFILE=LDT.par; #What's the name of the .par files in your bold/ directories?		PARFILE=LDT.par; #What's the name of the .par files in your bold/ directories?

192.168.1.1 at 17:35, 31 October 2017

2017-10-31T17:35:20Z

← Older revision		Revision as of 13:35, 31 October 2017
Line 10:		Line 10:
	HEMIS=( lh rh ); #for automatically looping over both hemispheres		HEMIS=( lh rh ); #for automatically looping over both hemispheres
	PARFILE=LDT.par; #What's the name of the .par files in your bold/ directories?		PARFILE=LDT.par; #What's the name of the .par files in your bold/ directories?
	~~SKIPS=4; #If you wish to drop the first n volumes, set to some value other than 0~~
	ANROOT="LDT.sm" #base name for the analysis directories		ANROOT="LDT.sm" #base name for the analysis directories

Line 27:		Line 26:
	-mcextreg \		-mcextreg \
	-TR ${TR} \		-TR ${TR} \
	~~-nskip ${SKIPS} \~~
	-refeventdur ${REFEVENTDUR} \		-refeventdur ${REFEVENTDUR} \
	-analysis ${ANROOT}${SMOOTHING}.${hemi} \		-analysis ${ANROOT}${SMOOTHING}.${hemi} \
Line 35:		Line 33:

	This step creates analysis directories in your $SUBJECTS_DIR containing single files that contain all the information needed for the next step.		This step creates analysis directories in your $SUBJECTS_DIR containing single files that contain all the information needed for the next step.

			Note that there is also a directive to skip volumes, however it doesn't seem to do what we expect it to, and so we just drop those volumes from the data entirely, and modify the event onsets to account for the dropped volumes.