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Icasso #294

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Icasso #294

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db6de73
Added --ica-method=ICASSO option to hcp_fix_multi_run, which substitu…
Jun 6, 2024
9e90a81
expanded comments
Jun 6, 2024
54dc9c7
Restored IcaFix example script to default parameters except that ICAm…
Jun 6, 2024
3fcdf25
remove stray debugging line
Jun 6, 2024
f209487
restored default settings file path
Jun 6, 2024
0df3d65
fixed example inputs
Jun 6, 2024
5858138
fixed comment
Jun 6, 2024
d8dc523
put savefig in try-catch for octave
Jun 7, 2024
764724f
corrected spaces vs tabs mismatch
Jun 8, 2024
d37929c
Removed tr, made mix and Tmodes equivalency explicit, moved [pcaE,pca…
Jun 11, 2024
40cd2c6
Added IO dependency checking and switching.Spun off mixture modeling …
Jul 9, 2024
39cb7ef
cleaned up comments
Jul 9, 2024
504ba89
Fixed cifti handling. Improved error checking and comments.I think it…
Jul 9, 2024
bb92d46
now saves icasso figures for each icasso level
Jul 9, 2024
3d4cf23
now saves icasso figures for each icasso level
Jul 9, 2024
24543fd
check IO dependencies earlier, use system instead for unix, renamed r…
Jul 10, 2024
fedad95
Removed redundant nClust argument and removed orphan comments.
Jul 12, 2024
3e28842
hcp_multirun_fix: fixed run_icasso arguments. mixtureModel: changed h…
Jul 12, 2024
431ef23
mixtureModel now sends shell outputs to console and errors out if any…
Jul 26, 2024
dd4347e
remove a troubleshooting foo
Jul 26, 2024
9ba3a51
fix io in run_icasso, remove extra s from parameter name in hcp_fix_m…
Oct 7, 2024
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5 changes: 4 additions & 1 deletion Examples/Scripts/IcaFixProcessingBatch.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,9 @@ main() {
# set whether or not to regress motion parameters (24 regressors)
# out of the data as part of FIX (TRUE or FALSE)
domot=FALSE

# set the ICA Method (MELODIC or ICASSO)
ICAmethod=MELODIC

# set the training data used in multi-run fix mode
MRTrainingData=HCP_Style_Single_Multirun_Dedrift.RData
Expand Down Expand Up @@ -233,7 +236,7 @@ main() {

echo " InputFile: ${InputFile}"

cmd=("${queuing_command[@]}" "${HCPPIPEDIR}/ICAFIX/hcp_fix_multi_run" --fmri-names="${InputFile}" --high-pass=${bandpass} --concat-fmri-name="${ConcatFileName}" --motion-regression=${domot} --training-file="${MRTrainingData}" --fix-threshold=${FixThreshold} --delete-intermediates="${DeleteIntermediates}" --config="$config" --processing-mode="$processingmode")
cmd=("${queuing_command[@]}" "${HCPPIPEDIR}/ICAFIX/hcp_fix_multi_run" --fmri-names="${InputFile}" --high-pass=${bandpass} --concat-fmri-name="${ConcatFileName}" --motion-regression=${domot} --training-file="${MRTrainingData}" --fix-threshold=${FixThreshold} --delete-intermediates="${DeleteIntermediates}" --config="$config" --processing-mode="$processingmode" --ica-method="$ICAmethod")
echo "About to run: ${cmd[*]}"
"${cmd[@]}"
done
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