Watch this space for an update on MSMAll with MultiRunFIX. The pipelines
in the current master aren¹t all working together and we are working on
fixing that.
Matt.
On 10/9/18, 9:58 AM, "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:
>
>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 I¹m just wondering that I should run fMRISurfacePipeline for
>MultiRunICAFIX-cleaned data.
>
>This might be silly question as I don¹t 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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