Here is the error:
readlink: illegal option -- f usage: readlink [-n] [file ...] I believe Tim already gave you instructions for this. Also, the log_Warn line is again concerning as to whether you followed the installation instructions and all version 4.0.0 files here. Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Monday, April 15, 2019 at 8:53 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Brown, Tim" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>> Subject: Re: [HCP-Users] DeDriftAndResamplePipeline error I had to re-run DeDriftAndResamplePipeline twice because it was searching for settings.sh in the wrong place, and now I am getting the following error message: ReApplyFixMultiRunPipeline.sh: line 586: log_Warn: command not found I am attaching log files. Does the folder containing fix1.067 need to include all the ICAFIX files? Thanks a lot! Leah. On Apr 15, 2019, at 12:19 AM, Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> wrote: It seams to be working now. Thanks a lot! Leah. On Apr 15, 2019, at 12:04 AM, Glasser, Matthew <glass...@wustl.edu<mailto: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 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 ________________________________ 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. ________________________________ 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. ________________________________ 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
