Is this with single run or multi-run FIX? Did you get any errors?
Matt.
On 10/5/18, 6:16 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim" <hcp-users-boun...@humanconnectome.org on behalf of
sykim...@gmail.com> wrote:
>Dear Experts:
>
>We¹re 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 couldn¹t 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@rfM
>RI_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="${HCPPIPEDIR}/global/templates/MSMAll/DeDriftingGroup.L.s
>phere.DeDriftMSMAll.164k_fs_LR.surf.gii@${HCPPIPEDIR}/global/templates/MSM
>All/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
>${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii. That¹s why I¹m
>confused with our output.
>
>I wonder that the output "${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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