biac:fsl:guide
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biac:fsl:guide [2012/12/12 17:54] – [III. Writing a batch script for FSL] petty | biac:fsl:guide [2024/06/21 15:44] (current) – external edit 127.0.0.1 | ||
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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}/ | ||
######### | ######### | ||
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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 ======= | + | |
- | + | ||
- | Intermittent crashes on golgi, often suggesting an "out of memory" | + | |
- | + | ||
- | + | ||
- | + | ||
- | ===== Registration ===== | + | |
- | + | ||
- | Registration is very poor for many of the spiral images | + | |
- | * Should we correct for maximum image intensity in some way? | + | |
- | * Do we use ORIENT files? Registration seems dubious. | + | |
- | + | ||
- | It may be the case that if there is less than 120mm in any direction, then it will pop up the " | + | |
- | + | ||
- | ===== Using ORIENT Files ===== | + | |
- | + | ||
- | The ORIENT file created by Syam Gyadde seems to give better registration results for data acquired with both spiral and EPI sequences. The file is a .mat file located in / | + | |
- | + | ||
- | == ORIENT in template.fsf == | + | |
- | The last section of the template.fsf should read as follows: | + | |
- | + | ||
- | < | + | |
- | # Alternative example_func image (not derived from input 4D dataset) | + | |
- | set fmri(alternative_example_func) "" | + | |
- | + | ||
- | # Delete GLM residuals? | + | |
- | set fmri(cleanup_residuals_yn) 1 | + | |
- | + | ||
- | # Initial structural space registration initialisation transform | + | |
- | set fmri(init_initial_highres) "" | + | |
- | + | ||
- | # Structural space registration initialisation transform | + | |
- | set fmri(init_highres) "" | + | |
- | + | ||
- | # Standard space registration initialisation transform | + | |
- | set fmri(init_standard) " | + | |
- | + | ||
- | == ORIENT in batchFSL == | + | |
- | + | ||
- | * Before the **for** loop in the batch script begins, paste the following line: | + | |
- | + | ||
- | < | + | |
- | / | + | |
- | ORIENT=$FSLDATADIR/ | + | |
- | + | ||
- | * You will also need to define the variable name **ORIENT** in your sed list: | + | |
- | < | + | |
- | + | ||
- | + | ||
- | ===== MELODIC ICA ===== | + | |
- | + | ||
- | + | ||
- | ===== Second-level Analyses ===== | + | |
- | + | ||
- | ====== Troubleshooting ====== | ||
- | === Registration problems: === | ||
- | * Problem: the data is being registered as a large, stretched-out brain, going way beyond the bounds of a normal brain | ||
- | * Solution: check the .bxh header files for your original functional data. The scanner has recently been putting out functional images with voxel sizes for anatomical images. | ||
- | * Problem: the brain is being flipped so that the frontal lobe is near the cerebellum | ||
- | * Solution: run a BET brain extraction on the anatomical data. See step 5 in the [[biac: | ||
- | === FEAT errors === | ||
- | * Problem: while running a batch script, all of the FEAT windows pop up at once even though the script is supposed to run them sequencially | ||
- | * Solution: open the script using nedit and find the line that starts with **feat** followed by some input files. | ||
- | * Problem: when running a batch script, the FEAT Watcher says that the number of volumes is 0 | ||
- | * Solution: your script is pointing to a file that doesn' | ||
- | * Problem: when running a batch script, the FEAT Watcher says that the number of volumes is incorrect (not 0, see above) | ||
- | * Solution: the batch script is most likely using a template file that assumes that all of your runs have the same number of time points. | ||
- | * Problem: the run stopped, saying the problem was possibly golgi ran out of memory | ||
- | * Solution: |
biac/fsl/guide.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1