Issue when running MSMAllPipeline.sh

[Yonatan Abrham]

I'm trying to run the MSMAllPipeline.sh pipeline on one subject from the HCP_EP data and I get the following error(towards the end below). Would you be able to help with this issue? the directory exists and contains other outputs.

ERROR: failed to open file '/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii', file does not exist, or folder permissions prevent seeing it

##Below is the same log but it includes the MSMAll.sh##

Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Cannot reliably show an msm version because some versions of msm do not support a --version option
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Using named parameters
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Study Folder:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Subject: sub-C1081
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: High Res Mesh: 164
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Low Res Mesh: 32
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Output fMRI Name: Task_Rest_All
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: fMRI Proc STRING: _Atlas_hp2000_clean_vn
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Input PCA Registration Name: MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Input Registration Name: MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Registration Name Stem: MSMAll_InitalReg
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSN Target File: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_dREPLACEDIM_ROW_vn/melodic_oIC.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSN Cost Weights: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_dREPLACEDIM_ROW_vn/Weights.txt
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Myelin Target File: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Topography ROI File: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.atlas_Topographic_ROIs.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Topography Target File: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.atlas_Topography.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Iterations: CA_CAT
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Method:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Use MIGP: NO
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: ICA Dim: 40
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Regression Params: 7_8_9_10_11_12_13_14_15_16_17_18_19_20_21
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: VN:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: ReRun: YES
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Reg Conf: /opt/HCP/HCPpipelines/MSMConfig/MSMAllStrainFinalconf1to1_1to3
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Reg Conf Vars: NONE
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: MATLAB run mode: 1
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: StudyFolder: /mnt/0/data/sub-C1081/preprocessed/
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Subject: sub-C1081
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: HighResMesh: 164
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: LowResMesh: 32
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: OutputfMRIName: Task_Rest_All
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: fMRIProcSTRING: _Atlas_hp2000_clean_vn
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: InPCARegName: MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: InRegName: MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RegNameStem: MSMAll_InitalReg
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSNTargetFileOrig: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_dREPLACEDIM_ROW_vn/melodic_oIC.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSNCostWeightsOrig: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_dREPLACEDIM_ROW_vn/Weights.txt
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: MyelinTargetFile: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: TopographyROIFile: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.atlas_Topographic_ROIs.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: TopographyTargetFile: /opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.atlas_Topography.32k_fs_LR.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Iterations: CA_CAT
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Method: WRN
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: UseMIGP: NO
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: ICAdim: 40
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RegressionParams: 7_8_9_10_11_12_13_14_15_16_17_18_19_20_21
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: VN: NO
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: ReRun: YES
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RegConf: /opt/HCP/HCPpipelines/MSMConfig/MSMAllStrainFinalconf1to1_1to3
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RegConfVars: NONE
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: MatlabRunMode: 1
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Caret7_Command: /opt/workbench/workbench/bin_rh_linux64/wb_command
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: AtlasFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: DownSampleFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: NativeFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/Native
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: ResultsFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/Results/Task_Rest_All
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: T1wFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/T1w
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: DownSampleT1wFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/T1w/fsaverage_LR32k
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: NativeT1wFolder: /mnt/0/data/sub-C1081/preprocessed//sub-C1081/T1w/Native
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: LowICAdims: 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Iterations: CA CAT
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: NumIterations: 2
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: CorrectionSigma: 14.14213562373095048801
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: BC: NO
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: nTPsForSpectra: 0
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: VolParams: NO
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSNTargetFile: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: File: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii EXISTS
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RSNCostWeights: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: File: /opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt EXISTS
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: InPCARegName is MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: InPCARegString: MSMSulc
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: OutPCARegString:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: PCARegString:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: SurfRegSTRING:
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Check for existence of of normalized midthickness Vertex Area map
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Normalized midthickness VA file already exists
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: NumIterations: 2
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: i: 1
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: RegName: MSMAll_InitalReg_1_d40_WRN
Tue Jun  7 14:50:18 EDT 2022:MSMAll.sh: Modalities: CA
Tue Jun  7 14:50:21 EDT 2022:MSMAll.sh: Modalities includes C
Tue Jun  7 14:50:21 EDT 2022:MSMAll.sh: Resample the atlas instead of the timeseries
Tue Jun  7 14:50:23 EDT 2022:MSMAll.sh: addpath '/opt/HCP/HCPpipelines/global/matlab/cifti-matlab'; addpath '/opt/HCP/HCPpipelines/global/matlab'; addpath '/opt/HCP/HCPpipelines/MSMAll/scripts'; MSMregression('/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.atlas_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii','/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/Results/Task_Rest_All/Task_Rest_All_Atlas_hp2000_clean_vn.dtseries.nii','/opt/HCP/HCPpipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt','/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR','/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_weights.32k_fs_LR.dscalar.nii','/opt/workbench/workbench/bin_rh_linux64/wb_command','WRN','/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/Native/MSMAll_InitalReg_1_d40_WRN/Params.txt','NO',0,'NO','NO');
/opt/HCP/HCPpipelines/MSMAll/scripts/MSMAll.sh: line 728: matlab: command not found
Tue Jun  7 14:50:23 EDT 2022:MSMAll.sh: Resample the individual maps so they are in the correct space

While running:
/opt/workbench/workbench-1.5.0/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-resample /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii COLUMN /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii COLUMN ADAP_BARY_AREA ENCLOSING_VOXEL /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii -surface-postdilate 40 -left-spheres /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.L.sphere.MSMSulc.32k_fs_LR.surf.gii /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.L.sphere.32k_fs_LR.surf.gii -left-area-surfs /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.L.midthickness.32k_fs_LR.surf.gii /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.L.midthickness.32k_fs_LR.surf.gii -right-spheres /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.R.sphere.MSMSulc.32k_fs_LR.surf.gii /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.R.sphere.32k_fs_LR.surf.gii -right-area-surfs /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.R.midthickness.32k_fs_LR.surf.gii /mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.R.midthickness.32k_fs_LR.surf.gii

ERROR: failed to open file '/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii', file does not exist, or folder permissions prevent seeing it

Thank you in advance,

Yonatan

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[Coalson, Timothy Scott (S&T-Student)]

The actual first error message is this line:

/opt/HCP/HCPpipelines/MSMAll/scripts/MSMAll.sh: line 728: matlab: command not found

You can install the free MCR runtime of the appropriate version (2017b, 9.3), edit the SetUp... to point to where it is installed, then try the script in compiled matlab mode (0).

Tim

---

From: Yonatan Abrham <yabr...@gmail.com>
Sent: Tuesday, June 7, 2022 2:12 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Issue when running MSMAllPipeline.sh

 

WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.

Greetings,

I'm trying to run the MSMAllPipeline.sh pipeling on one subject from the HCP_EP data and I get the following error(towards the end below). Would you be able to help with this issue? the directory exists and contains other outputs.

ERROR: failed to open file '/mnt/0/data/sub-C1081/preprocessed//sub-C1081/MNINonLinear/fsaverage_LR32k/sub-C1081.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii', file does not exist, or folder permissions prevent seeing it

##Below is the same log but in it includes the MSMAll.sh##

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[Yonatan Abrham]

Thank you very much. I didn't see that message. I'm using Qunex and MATLAB_COMPILER_RUNTIME=/opt/matlab/v93 in my environment. I will set --matlab-run-mode=0 and try it again.

Sincerely,

Yonatan

[Harms, Michael]

 

QuNex should default to using compiled matlab mode, and you shouldn’t need to mess with any environment variables related to matlab inside the container.  That is already all taken care of for users.

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: Yonatan Abrham <yabr...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, June 7, 2022 at 4:46 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "tsc...@mst.edu" <tsc...@mst.edu>
Subject: Re: [hcp-users] Issue when running MSMAllPipeline.sh

 

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[Yonatan Abrham]

It worked and finished, many thanks again. I had to use compiled matlab mode.

Thank you,

Yonatan

[Jure Demsar]

Hi Yonatan,

I am the QuNex development lead. Did you run the MSMAll pipeline through a QuNex command or did you just use the environment inside the QuNex container and ran the command through HCP pipelines that are installed in there? If you used a QuNex command, could you please post it here so I can debug on our end, thanks! This is weird since QuNex uses compiled MATLAB as a default.

Cheers, Jure

[Yonatan Abrham]

Hi Jure,

I didn't use the Qunex commands. I used the qunex_environment.sh to set the environment and then run the command through the HCP pipelines.

Thank you,

Yonatan

[Harms, Michael]

 

Glad you got it working.  I’d suggest you look into actually running the HCPpipelines with the various QuNex commands.  It adds a “layer” relative to calling the HCPpipelines scripts directly, but there are various benefits – e.g., harmonized argument names for calling the HCPpipeline scripts, automatic generation of log files, etc.

[Yonatan Abrham]

Thank you very much. I will surely follow through with your suggestion. 

Thank you,

Yonatan