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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users