It seams to be working now. Thanks a lot! Leah.
> On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > > If you ran MR+FIX, you need to set these appropriately > > MRFixConcatName="NONE" > MRFixNames="NONE" > > And not set > > fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE > > https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh > > <https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/DeDriftAndResamplePipelineBatch.sh> > > Also it looks like line 124 needs an “s” on the end of the flag name to read > --multirun-fix-concat-names=${MRFixConcatName} > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday, April 14, 2019 at 10:56 PM > To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Cc: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error > > Thanks a lot for your response. > > I am running v.4.0.0 now. And I have set up the script as follow: > > HighResMesh="164" > LowResMesh="32" > RegName="MSMAll_InitalReg_2_d40_WRN" > DeDriftRegFiles="${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" > ConcatRegName="MSMAll_Test" > Maps="sulc curvature corrThickness thickness" > MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied > MRFixConcatName="NONE" > MRFixNames="NONE" > #fixNames="rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL" > #Space delimited list or NONE > fixNames="RS_fMRI_1 RS_fMRI_2" #Space delimited list or NONE > #dontFixNames="tfMRI_WM_LR tfMRI_WM_RL tfMRI_GAMBLING_LR tfMRI_GAMBLING_RL > tfMRI_MOTOR_LR tfMRI_MOTOR_RL tfMRI_LANGUAGE_LR tfMRI_LANGUAGE_RL > tfMRI_SOCIAL_LR tfMRI_SOCIAL_RL tfMRI_RELATIONAL_LR tfMRI_RELATIONAL_RL > tfMRI_EMOTION_LR tfMRI_EMOTION_RL" #Space delimited list or NONE > dontFixNames="NONE" > SmoothingFWHM="2" #Should equal previous grayordinates smoothing (because we > are resampling from unsmoothed native mesh timeseries) > HighPass="0" > MotionRegression=TRUE > MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 > octave > #MatlabMode="0" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 > octave > > But the script does not run and it is aborted with the following message: > DeDriftAndResamplePipeline.sh - ABORTING: unrecognized option: > --multirun-fix-concat-name=NONE > > I am attaching the log files. > > Leah. > > >> On Apr 14, 2019, at 11:10 PM, Glasser, Matthew <glass...@wustl.edu >> <mailto:glass...@wustl.edu>> wrote: >> >> In this case you do run it with the individual fMRI names and that doesn’t >> look like the version 4.0.0 example script... >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org >> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno >> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> >> Date: Sunday, April 14, 2019 at 10:06 PM >> To: HCP Users <hcp-users@humanconnectome.org >> <mailto:hcp-users@humanconnectome.org>> >> Subject: [HCP-Users] DeDriftAndResamplePipeline error >> >> Dear Experts, >> >> I have run DeDriftAndResamplePipelineBatch.sh from from >> ${StudyFolder}/${Subject}/scripts after running MSMAII and getting the >> following error: >> >> While running: >> /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command >> -metric-resample >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR.L.native.func.gii >> >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.sphere.MSMAll_Test.native.surf.gii >> >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/fsaverage_LR32k/NTTMS_s002_170812.L.sphere.32k_fs_LR.surf.gii >> ADAP_BARY_AREA >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_MSMAll_Test.L.atlasroi.32k_fs_LR.func.gii >> -area-surfs >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/Native/NTTMS_s002_170812.L.midthickness.native.surf.gii >> >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/T1w/fsaverage_LR32k/NTTMS_s002_170812.L.midthickness_MSMAll_Test.32k_fs_LR.surf.gii >> -current-roi >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Native/NTTMS_s002_170812.L.roi.native.shape.gii >> >> ERROR: NAME OF FILE: RS_fMRI_MR.L.native.func.gii >> PATH TO FILE: >> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR >> >> File does not exist. >> >> I set up the script DeDriftAndResamplePipelineBatch.sh as follow >> (rfMRINames=“RS_fMRI_MRâ€, the concatenated name from MR+FIX): >> >> 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" >> ConcatRegName="MSMAll_Test" >> Maps="sulc curvature corrThickness thickness" >> MyelinMaps="MyelinMap SmoothedMyelinMap" #No _BC, this will be reapplied >> rfMRINames="RS_fMRI_MR" #Space delimited list or NONE >> tfMRINames="NONE" >> SmoothingFWHM="2" #Should equal previous grayordiantes smoothing (because we >> are resampling from unsmoothed native mesh timeseries >> HighPass="0" >> MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab >> >> I am attaching the log files. >> >> Thanks a lot! >> >> Leah. >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >> >> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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