Configure mkcontrast-sess - Revision history

Chris: /* mkcontrast-sess */

2021-05-25T15:36:26Z

mkcontrast-sess

← Older revision		Revision as of 11:36, 25 May 2021
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	The key thing is that the <u>'''a'''</u>ctivated and <u>'''c'''</u>ontrast weightings must sum to zero. Continuing with this example, to configure the words > nonwords contrast for the analysis specified by the previous call to <code>mkanalysis-sess</code>, you would run the following command within your $SUBJECTS_DIR:		The key thing is that the <u>'''a'''</u>ctivated and <u>'''c'''</u>ontrast weightings must sum to zero. Continuing with this example, to configure the words > nonwords contrast for the analysis specified by the previous call to <code>mkanalysis-sess</code>, you would run the following command within your $SUBJECTS_DIR:
	mkcontrast-sess -analysis LDT.sm6.lh -contrast words-v-nonwords -a 2 -a 3 -c 1		mkcontrast-sess -analysis LDT.sm6.lh -contrast words-v-nonwords -a 2 -a 3 -c 1
			When you run this command, because we have two activated conditions and one contrast condition, the activated conditions will each be assigned a weight of +0.5, and the single contrast condition will be assigned a weight of -1.0: (+0.5) + (+0.5) + (-1.0) = 0.0

	Pertinent to some of our borrowed data, we have the following conditions for the children's dyslexia study:		Pertinent to some of our borrowed data, we have the following conditions for the children's dyslexia study:

Chris: /* Before You Start */

2021-05-25T15:32:02Z

Before You Start

← Older revision		Revision as of 11:32, 25 May 2021
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	The procedures that follow have a few dependencies:		The procedures that follow have a few dependencies:
	#You know the numerical codes associated with each of your conditions of interest in your .par files		#You know the numerical codes associated with each of your conditions of interest in your .par files
	#You have set the MATLAB environment variable (mkcontrast-sess will fail with an uninformative "Unknown variable" error message ~~otherwise~~		#You have set the MATLAB environment variable (mkcontrast-sess will otherwise fail with an uninformative "Unknown variable" error message)
	===Setting the MATLAB environment variable===		===Setting the MATLAB environment variable===
	set MATLAB=`getmatlab` #ALSO: set MATLAB=1 works		set MATLAB=`getmatlab` #ALSO: set MATLAB=1 works

Chris at 15:31, 25 May 2021

2021-05-25T15:31:38Z

← Older revision		Revision as of 11:31, 25 May 2021
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	Contrasts are planned comparisons reflecting hypotheses that you want to test. They are linear combinations of conditions. In order to construct a contrast, you need to know the numeric ID associated with each condition; this is specified in your [[Par-Files\|paradigm file]].		Contrasts are planned comparisons reflecting hypotheses that you want to test. They are linear combinations of conditions. In order to construct a contrast, you need to know the numeric ID associated with each condition; this is specified in your [[Par-Files\|paradigm file]].
			==Before You Start==
			The procedures that follow have a few dependencies:
			#You know the numerical codes associated with each of your conditions of interest in your .par files
			#You have set the MATLAB environment variable (mkcontrast-sess will fail with an uninformative "Unknown variable" error message otherwise
			===Setting the MATLAB environment variable===
			set MATLAB=`getmatlab` #ALSO: set MATLAB=1 works
			export MATLAB

			==mkcontrast-sess==
	Suppose, for example, your par-files for the LDT experiment were encoded with the following conditions:		Suppose, for example, your par-files for the LDT experiment were encoded with the following conditions:
	1 nonword		1 nonword

Chris at 14:37, 14 October 2020

2020-10-14T14:37:27Z

← Older revision		Revision as of 10:37, 14 October 2020
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	This should be a straightforward script to run, however this script relies on Matlab or Octave. After updating my FreeSurfer distribution to 7.1.1 (from version 6.0) I ran into the <code>MATLAB: Undefined variable</code> problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here], which I had never had before. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:		This should be a straightforward script to run, however this script relies on Matlab or Octave. After updating my FreeSurfer distribution to 7.1.1 (from version 6.0) I ran into the <code>MATLAB: Undefined variable</code> problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here], which I had never had before. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:
	MATLAB=`getmatlab`		MATLAB=`getmatlab`

			[[Category: FreeSurfer]]

Chris: /* Possible Problems */

2020-10-14T14:36:44Z

Possible Problems

← Older revision		Revision as of 10:36, 14 October 2020
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	./do_mkcontrast.sh FAM sm4		./do_mkcontrast.sh FAM sm4
	=Possible Problems=		=Possible Problems=
	This should be a straightforward script to run, however this script relies on Matlab or Octave. I ~~recently~~ ran into the <code>MATLAB: Undefined variable</code> problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:		This should be a straightforward script to run, however this script relies on Matlab or Octave. After updating my FreeSurfer distribution to 7.1.1 (from version 6.0) I ran into the <code>MATLAB: Undefined variable</code> problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here], which I had never had before. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:
	MATLAB=`getmatlab`		MATLAB=`getmatlab`

Chris: /* Possible Problems */

2020-10-14T14:35:38Z

Possible Problems

← Older revision		Revision as of 10:35, 14 October 2020
Line 54:		Line 54:
	./do_mkcontrast.sh FAM sm4		./do_mkcontrast.sh FAM sm4
	=Possible Problems=		=Possible Problems=
	This should be a straightforward script to run, however this script relies on Matlab or Octave. I recently ran into the problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:		This should be a straightforward script to run, however this script relies on Matlab or Octave. I recently ran into the <code>MATLAB: Undefined variable</code> problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:
	MATLAB=`getmatlab`		MATLAB=`getmatlab`

Chris: /* Possible Problems */

2020-10-14T14:34:42Z

Possible Problems

← Older revision		Revision as of 10:34, 14 October 2020
Line 54:		Line 54:
	./do_mkcontrast.sh FAM sm4		./do_mkcontrast.sh FAM sm4
	=Possible Problems=		=Possible Problems=
	This should be a straightforward script to run, however this script relies on Matlab or Octave. I recently ran into the ~~same~~ problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:		This should be a straightforward script to run, however this script relies on Matlab or Octave. I recently ran into the problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:
	MATLAB=`getmatlab`		MATLAB=`getmatlab`

Chris at 14:34, 14 October 2020

2020-10-14T14:34:15Z

← Older revision		Revision as of 10:34, 14 October 2020
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	Contrasts are ~~embodiments of~~ hypotheses that you want to test. They are linear combinations of conditions. In order to construct a contrast, you need to know the numeric ID associated with each condition; this is specified in your [[Par-Files\|paradigm file]].		Contrasts are planned comparisons reflecting hypotheses that you want to test. They are linear combinations of conditions. In order to construct a contrast, you need to know the numeric ID associated with each condition; this is specified in your [[Par-Files\|paradigm file]].

	Suppose, for example, your par-files for the LDT experiment were encoded with the following conditions:		Suppose, for example, your par-files for the LDT experiment were encoded with the following conditions:
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	I would run it thus:		I would run it thus:
	./do_mkcontrast.sh FAM sm4		./do_mkcontrast.sh FAM sm4
			=Possible Problems=
			This should be a straightforward script to run, however this script relies on Matlab or Octave. I recently ran into the same problem described [https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62907.html here]. The solution was to define a MATLAB variable. I modified my .bashrc file to include the following line, though you can also run it at the commandline just prior to running mkcontrast-sess:
			MATLAB=`getmatlab`

Chris: /* do_mkcontrast.sh */

2020-10-07T14:42:14Z

do_mkcontrast.sh

← Older revision		Revision as of 10:42, 7 October 2020
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	done		done

	After making this script executable with the chmod command, I would run it thus:		After making this script executable with the chmod command:
	./do_mkcontrast FAM sm4		chmod ugo+x do_mkcontrast.sh
			I would run it thus:
			./do_mkcontrast.sh FAM sm4

Chris: /* do_mkcontrast.sh */

2019-06-29T13:24:18Z

do_mkcontrast.sh

← Older revision		Revision as of 09:24, 29 June 2019
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	==do_mkcontrast.sh==		==do_mkcontrast.sh==
	Here's an example script:		Here's an example script:
	!#/bin/bash		#!/bin/bash
	PARADIGM=$1 #the first parameter is the PAR-file name		PARADIGM=$1 #the first parameter is the PAR-file name
	#e.g., when using FAM.par, I would pass "FAM" as the first parameter		#e.g., when using FAM.par, I would pass "FAM" as the first parameter