Dear Experts:
I have a question for MSMAll alignment for MultiRunICAFIX cleaned data.
Once I run the MultiRunICAFIX pipeline, I get the output like
"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii".
But I want to align the data (e.g.,
${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii) using MSMAll pipeline.
Running MSMAllPipeline script with above data seems to be fine without any
error. However, if I run DeDriftAndResamplePipeline script,
it requires ${fMRIConcatName}.${Hemisphere}.native.func.gii, which is absent in
${fMRIConcatName} folder.
I can generate ${fMRIConcatName}.${Hemisphere}.native.func.gii using
fMRISurfacePipeline.
But I’m just wondering that I should run fMRISurfacePipeline for
MultiRunICAFIX-cleaned data.
This might be silly question as I don’t clearly understand MSMAllPipeline and
DeDriftAndResamplePipeline.
Is there a method to have MSMAll-aligned MultiRunICAFIX-cleaned data?
Below is the scripts that I ran:
## MultiRunICAFIX
StudyFolder="/Volumes/easystore/projects/HCP"
Subject="300"
ConcatName1="rfMRI_REST_Concat_Day1"
ConcatName2="rfMRI_REST_Concat_Day2"
ResultFolder="${StudyFolder}/${Subject}/MNINonlinear/Results"
ICAFIXscriptFolder="/Users/sang-young/projects/Pipelines_master/ICAFIX"
${ICAFIXscriptFolder}/hcp_fix_multi_run
${ResultFolder}/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz@${ResultFolder}/rfMRI_REST1_PA/rfMRI_REST1_PA.nii.gz@${ResultFolder}/rfMRI_REST2_AP/rfMRI_REST2_AP.nii.gz@${ResultFolder}/rfMRI_REST2_PA/rfMRI_REST2_PA.nii.gz
2000 ${ResultFolder}/${ConcatName1}/${ConcatName1}.nii.gz
${FSL_FIXDIR}/training_files/HCP_hp2000.RData
${ICAFIXscriptFolder}/hcp_fix_multi_run
${ResultFolder}/rfMRI_REST3_AP/rfMRI_REST3_AP.nii.gz@${ResultFolder}/rfMRI_REST3_PA/rfMRI_REST3_PA.nii.gz@${ResultFolder}/rfMRI_REST4_AP/rfMRI_REST4_AP.nii.gz@${ResultFolder}/rfMRI_REST4_PA/rfMRI_REST4_PA.nii.gz
2000 ${ResultFolder}/${ConcatName2}/${ConcatName2}.nii.gz
${FSL_FIXDIR}/training_files/HCP_hp2000.RData
##MSMAllPipeline
fMRINames="rfMRI_REST_Concat_Day1 rfMRI_REST_Concat_Day2"
OutfMRIName="rfMRI_REST"
HighPass="2000"
fMRIProcSTRING="_Atlas_hp2000_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1"
${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
--path=${StudyFolder} \
--subject=${Subject} \
--fmri-names-list=${fMRINames} \
--output-fmri-name=${OutfMRIName} \
--high-pass=${HighPass} \
--fmri-proc-string=${fMRIProcSTRING} \
--msm-all-templates=${MSMAllTemplates} \
--output-registration-name=${RegName} \
--high-res-mesh=${HighResMesh} \
--low-res-mesh=${LowResMesh} \
--input-registration-name=${InRegName} \
--matlab-run-mode=${MatlabMode}
Thanks.
Sang-Young
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