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biac:fsl:guide [2012/12/12 17:54] – [III. Writing a batch script for FSL] pettybiac: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.  They use the bash scripting language that golgi uses.  before you start it is recommended you read a little on bash scripting [[http://pegasus.rutgers.edu/~elflord/unix/bash-tute.html|here]].  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.  They use the bash scripting language that golgi uses.  before you start it is recommended you read a little on bash scripting [[http://pegasus.rutgers.edu/~elflord/unix/bash-tute.html|here]]. 
-This script will run FEAT analysis, but requires 1)converted anat and func files and 2) a template. See [[biac:fsl:guide#I.Preparing for FSL|I.Preparing for FSL]] for file conversion. Example template shown below in this section.+This script will run FEAT analysis, but requires 1)converted anat and func files and 2) a template. See [[biac:fsl:guide#I.Preparing for FSL|I.Preparing for FSL]] for file conversion. Example template shown below in this section.  This script would read a template file, and replace the anat/output/data directories, then run feat. This script would be for running the analysis on the machine you are currently logged in to ... it would not be for submitting the the gridengine. For example cluster scripts see: [[biac:cluster:examples|BIAC Cluster Sample Scripts]] 
 Here's a sample **batchFSL** script:  Here's a sample **batchFSL** script: 
 +
 <code bash>#!/bin/bash <code bash>#!/bin/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=$1
-FSLDATADIR=~/net/katz/data/Reward.01/Data/FSL/$SUBJ +EXPDIR=`findexp Reward.01` 
-ANATFILE=${FSLDATADIR}/anatb.nii+FSLDATADIR=${EXPDIR}/Data/FSL/${SUBJ} 
 +ANATFILE=${FSLDATADIR}/anat_brain.nii
    
 ######### #########
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 done done
 </code> </code>
- 
 ===== 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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 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/fsl/feat5/detail.html#higher|feat web manual]]. +There is a good description of concepts behind higher-level analyses on the [[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#Setting_Up_Higher-Level_Analysis_in_FEAT|feat higher level analyis]].
  
 ======= VI.Remaining Questions & Problems ======= ======= VI.Remaining Questions & Problems =======
biac/fsl/guide.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1