Dear Experts:
We’re acquiring HCP-style data, and running HCP pipelines. We are following the
order of pipelines as Matt suggested.
But I have concerns about final output of MSMAll pipeline for rfMRI data set.
Once we run the MSMAllPipeline and DeDriftAndResamplePipeline, we get final
output as "${fMRIName}_Atlas_MSMAll.dtseries.nii".
But I expected that the output would be
${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii, as HCP_S1200 release data.
I couldn’t find where it was wrong. Below is the variables that I set to run
MSMAllPipeline as well as DeDriftAndResamplePipeline.
***************************************************************
1. MSMAllPipeline
StudyFolder="/Volumes/easystore/projects/HCP"
Subjlist="264"
fMRINames="rfMRI_REST1_AP@rfMRI_REST1_PA@rfMRI_REST2_AP@rfMRI_REST2_PA@rfMRI_REST3_AP@rfMRI_REST3_PA@rfMRI_REST4_AP@rfMRI_REST4_PA"
OutfMRIName="rfMRI_REST"
HighPass="2000"
fMRIProcSTRING="_Atlas_hp2000_clean"
MSMAllTemplates="${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=${MatlabMode}
2. DeDriftAndResamplePipeline
StudyFolder="/Volumes/easystore/projects/HCP"
Subjlist="264"
HighResMesh="164"
LowResMesh="32"
RegName="MSMAll_InitalReg_2_d40_WRN"
DeDriftRegFiles="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"
oncatRegName="MSMAll"
Maps="sulc curvature corrThickness thickness"
MyelinMaps="MyelinMap SmoothedMyelinMap"
rfMRINames="rfMRI_REST1_AP rfMRI_REST1_PA rfMRI_REST2_AP rfMRI_REST2_PA
rfMRI_REST3_AP rfMRI_REST3_PA rfMRI_REST4_AP rfMRI_REST4_PA"
tfMRINames="tfMRI_WM_AP tfMRI_WM_PA tfMRI_MOTOR_AP tfMRI_MOTOR_PA"
SmoothingFWHM="2"
HighPass="2000"
MatlabMode="1"
${HCPPIPEDIR}/DeDriftAndResample/DeDriftAndResamplePipeline.sh \
--path=${StudyFolder} \
--subject=${Subject} \
--high-res-mesh=${HighResMesh} \
--low-res-meshes=${LowResMesh} \
--registration-name=${RegName} \
--dedrift-reg-files=${DeDriftRegFiles} \
--concat-reg-name=${ConcatRegName} \
--maps=${Maps} \
--myelin-maps=${MyelinMaps} \
--rfmri-names=${rfMRINames} \
--tfmri-names=${tfMRINames} \
--smoothing-fwhm=${SmoothingFWHM} \
--highpass=${HighPass} \
--matlab-run-mode=${MatlabMode}
*****************************************************************************
In HCP_S1200 released data, I can see two files, which are named as
${fMRIName}_Atlas_MSMAll.dtseries.nii and
${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii. That’s why I’m confused
with our output.
I wonder that the output "${fMRIName}_Atlas_MSMAll.dtseries.nii" generated by
above pipeline is also MSMAll aligned and cleaned cifti file?
Could anyone give me comments about what is wrong with my processing pipeline?
Thanks.
Sang-Young
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