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 17:59] – [V. Setting up Second-Level Analyses] 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. | ||
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====== V. Setting up Second-Level Analyses ====== | ====== V. Setting up Second-Level Analyses ====== | ||
- | * Bring up a Golgi window in F-Secure SSH. | ||
- | * **cd / | ||
* Type **fsl**. Click **FEAT**. | * Type **fsl**. Click **FEAT**. | ||
* Change the top left pull-down menu to **Higher-level analysis**. | * Change the top left pull-down menu to **Higher-level analysis**. | ||
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Your new analyses will be saved in a new directory called **across_runs.gfeat**. | Your new analyses will be saved in a new directory called **across_runs.gfeat**. | ||
- | There is a good description of concepts behind higher-level analyses on the [[http://www.fmrib.ox.ac.uk/ | + | There is a good description of concepts behind higher-level analyses on the [[http://fsl.fmrib.ox.ac.uk/ |
======= VI.Remaining Questions & Problems ======= | ======= VI.Remaining Questions & Problems ======= |
biac/fsl/guide.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1