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Yash refactor #254

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merged 21 commits into from
Dec 19, 2023
Merged

Yash refactor #254

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ff2dff1
add set -E to debug.shlib, cleanup and style
coalsont Nov 8, 2022
c9c2d82
Finsihed testing of prefreesurfer, with updates to pipeline scripts
ythackerCS Sep 18, 2023
8b78137
Finished testing of fMRIVolume along with pipeline scripts.
ythackerCS Sep 20, 2023
3d28db5
Cleaned up prefreesurfer comments that were unnecessary.
ythackerCS Sep 20, 2023
cf3cf99
Removed unecessary commented lines.
ythackerCS Sep 20, 2023
d7fc50d
Removed commented out opts parsing lines from fMIRVolume scripts
ythackerCS Sep 20, 2023
bf1e3e3
Finished testing of FMRISurface
ythackerCS Oct 12, 2023
6f22468
Postfix and ReapplyFix tested and run successfully.
ythackerCS Oct 20, 2023
5bdc932
Fixed all comments from github and commiting non-pipeline specific fi…
ythackerCS Nov 1, 2023
e979b4a
Addressed additional comments by Tim and removed old code.
ythackerCS Nov 3, 2023
274c93f
Addressed last few comments by Tim on msm and make avg.
ythackerCS Nov 4, 2023
f7ba047
various cleanup and fixes, help info displays at least
coalsont Nov 4, 2023
2b8668b
Additional cleanup
coalsont Nov 4, 2023
cc33ada
more cleanup
coalsont Nov 4, 2023
c128776
restore definition of script_name for info function
coalsont Nov 10, 2023
cdfa0c7
replace ls with glob, quoting
coalsont Nov 11, 2023
3f19971
remove stay opts_DefaultOpt
coalsont Nov 13, 2023
94cfc83
stop matlab from expecting binary .mat format from melodic_mix
coalsont Nov 13, 2023
f011bf8
set another load() to ascii, for safety
coalsont Nov 13, 2023
48c123a
Fixed an unbound variable issue in PostFix.
demsarjure Nov 16, 2023
84a6729
Make even/odd checking use Pos_Neg_b0
coalsont Nov 16, 2023
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2 changes: 1 addition & 1 deletion DeDriftAndResample/DeDriftAndResamplePipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -508,7 +508,7 @@ for fMRIName in ${fixNames[@]+"${fixNames[@]}"} ${dontFixNames[@]+"${dontFixName
${Caret7_Command} -metric-resample ${ResultsFolder}/${fMRIName}/${fMRIName}.${Hemisphere}.native.func.gii ${NativeFolder}/${Subject}.${Hemisphere}.sphere.${OutputRegName}.native.surf.gii ${DownSampleFolder}/${Subject}.${Hemisphere}.sphere.${LowResMesh}k_fs_LR.surf.gii ADAP_BARY_AREA ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii -area-surfs ${NativeT1wFolder}/${Subject}.${Hemisphere}.midthickness.native.surf.gii ${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness_${OutputRegName}.${LowResMesh}k_fs_LR.surf.gii -current-roi ${NativeFolder}/${Subject}.${Hemisphere}.roi.native.shape.gii
${Caret7_Command} -metric-dilate ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii ${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness_${OutputRegName}.${LowResMesh}k_fs_LR.surf.gii 30 ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii -nearest
${Caret7_Command} -metric-mask ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii ${DownSampleFolder}/${Subject}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.shape.gii ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii
Sigma=`echo "$SmoothingFWHM / ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) )" | bc -l`
Sigma=`echo "$SmoothingFWHM / (2 * sqrt(2 * l(2)))" | bc -l`
${Caret7_Command} -metric-smoothing ${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness_${OutputRegName}.${LowResMesh}k_fs_LR.surf.gii ${ResultsFolder}/${fMRIName}/${fMRIName}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii ${Sigma} ${ResultsFolder}/${fMRIName}/${fMRIName}_s${SmoothingFWHM}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii -roi ${DownSampleFolder}/${Subject}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.shape.gii
${Caret7_Command} -cifti-replace-structure ${ResultsFolder}/${fMRIName}/${fMRIName}_Atlas_${OutputRegName}.dtseries.nii COLUMN -metric ${Structure} ${ResultsFolder}/${fMRIName}/${fMRIName}_s${SmoothingFWHM}_${OutputRegName}.${Hemisphere}.atlasroi.${LowResMesh}k_fs_LR.func.gii
done
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