Re: [HCP-Users] DeDriftAndResamplePipeline error

[Marta Moreno]

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

DeDriftAndResamplePipeline.sh.e20908
Description: Binary data

DeDriftAndResamplePipeline.sh.o20908
Description: Binary data

On Apr 14, 2019, at 11:10 PM, Glasser, Matthew <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> on behalf of Marta Moreno <mmorenoort...@icloud.com> Date: Sunday, April 14, 2019 at 10:06 PM To: HCP Users <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_MR”, 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 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.