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biac:fsl:guide
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biac:fsl:guide [2012/12/12 17:55] petty [III. Writing a batch script for FSL] |
biac:fsl:guide [2012/12/12 17:59] petty [V. Setting up Second-Level Analyses] |
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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 | ||
| Line 133: | Line 135: | ||
| 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. | ||
| Line 171: | Line 172: | ||
| ====== 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**. | ||
| Line 184: | Line 183: | ||
| 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: 2023/02/23 18:43 (external edit)
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