Re: [HCP-Users] DeDriftAndResamplePipeline error

Mon, 15 Apr 2019 06:54:48 -0700

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.

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Attachment: DeDriftAndResamplePipeline.sh.e40867
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Attachment: DeDriftAndResamplePipeline.sh.o40867
Description: Binary data


On Apr 15, 2019, at 12:19 AM, Marta Moreno <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> 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

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>
Date: Sunday, April 14, 2019 at 10:56 PM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP Users <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> 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.

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