biac:fsl:guide
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biac:fsl:guide [2012/12/12 17:53] – [IV.Incorporating MELODIC analyses] petty | biac:fsl:guide [2012/12/12 17:58] – [III. Writing a batch script for FSL] petty | ||
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====== III. Writing a batch script for FSL ====== | ====== III. Writing a batch script for FSL ====== | ||
If you have a lot of subjects or many runs to do the same analysis to, you may want to run a batch script to avoid tediously running the the rather slow FSL GUI. Batch scripts should be written on golgi using nedit. | If you have a lot of subjects or many runs to do the same analysis to, you may want to run a batch script to avoid tediously running the the rather slow FSL GUI. Batch scripts should be written on golgi using nedit. | ||
- | This script will run FEAT analysis, but requires 1)converted anat and func files and 2) a template. See [[biac: | + | This script will run FEAT analysis, but requires 1)converted anat and func files and 2) a template. See [[biac: |
Here's a sample **batchFSL** script: | Here's a sample **batchFSL** script: | ||
+ | |||
<code bash># | <code bash># | ||
#for each subject you will have to modify this script for the number of runs and | #for each subject you will have to modify this script for the number of runs and | ||
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#change this part | #change this part | ||
SUBJ=$1 | SUBJ=$1 | ||
- | FSLDATADIR=~/ | + | EXPDIR=`findexp |
- | ANATFILE=${FSLDATADIR}/ | + | FSLDATADIR=${EXPDIR}/Data/FSL/${SUBJ} |
+ | ANATFILE=${FSLDATADIR}/ | ||
######### | ######### | ||
#makes the orient file | #makes the orient file | ||
- | / | ||
- | ORIENT=$FSLDATADIR/ | ||
for run in 01 02 03 04; do | for run in 01 02 03 04; do | ||
| | ||
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sed -e ' | sed -e ' | ||
-e ' | -e ' | ||
- | -e ' | ||
-e ' | -e ' | ||
done | done | ||
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done | done | ||
</ | </ | ||
- | |||
===== making a template .fsf file ===== | ===== making a template .fsf file ===== | ||
when making a batch file, you need to have a template file that has the outline for your FEAT analysis. | when making a batch file, you need to have a template file that has the outline for your FEAT analysis. |
biac/fsl/guide.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1