Make sure you have the whole pipelines repo for 4.0.0, do not try to mix and match folders from different versions, and make sure your setup script is pointed to the 4.0.0 version when running things from 4.0.0. The log_Warn function is defined inside global/scripts, and it should get sourced automatically based on HCPPIPEDIR, so make sure that is set correctly (pointed to the 4.0.0 version).
Tim
Thanks for your response. And sorry to bother again with this issue but I am still getting the following error: ReApplyFixMultiRunPipeline.sh: line 592: log_Warn: command not found
Please find log files attached.
Pipelines for MR+FIX, MSMAll and DeDriftAndResample are from version version 4.0.0. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface are from version 3_22 Since MR+FIX and MSMAll were run successfully, why it should be a version issue in ReApplyFixMultiRunPipeline.sh?
I want to be sure this is a version issue because I have already run PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface version 3_22 on a sample of 30 patients pre/post tx.
Thanks a lot for your help and patience.
Leah.
I would also suggest changing your log level to INFO in wb_view, preferences (the wb_command option does not store the logging level change to preferences). We should probably change the default level, or change the level of that volume coloring message.
Tim
On Mon, Apr 15, 2019 at 8:34 PM Timothy Coalson < tsc...@mst.edu> wrote: I have pushed a similar edit to reapply MR fix, please update to the latest master.
Tim
On Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson < tsc...@mst.edu> wrote: They weren't instructions, I pushed an edit, and it was a different script.
Tim
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.
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.
It seams to be working now. Thanks a lot!
Leah.
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
Also it looks like line 124 needs an “s” on the end of the flag name to read --multirun-fix-concat-names=${MRFixConcatName}
Matt.
Thanks a lot for your response.
I am running v.4.0.0 now. And I have set up the script as follow:
HighResMesh="164"
LowResMesh="32"
RegName="MSMAll_InitalReg_2_d40_WRN"
DeDriftRegFiles="${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.
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.
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.
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DeDriftAndResamplePipeline.sh.e42974