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Processing pipelines for the HCP
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Want to further removing noise #316

Open RuiWang0805 opened 1 week ago

RuiWang0805 commented 1 week ago

Hi, After finishing the minimally preprocessed the series data for fMRI (denoising based on the ICA-fix algorithm) and dMRI, I want to further remove noise, How can I choose the way for denoising noise? Hope to recommend a more common way of noise reduction. Hope your reply!

glasserm commented 1 week ago

For fMRI, you can also remove global respiratory artifact using temporal ICA. For unstructured noise, we recommend parcellation. We are working on other methods for non-parcellated analyses, but have not yet published detailed guidelines on that.

RuiWang0805 commented 1 week ago

For fMRI, you can also remove global respiratory artifact using temporal ICA. For unstructured noise, we recommend parcellation. We are working on other methods for non-parcellated analyses, but have not yet published detailed guidelines on that.

Hello, I have a question the CPU of my personal computer is 20 cores and 28 threads. During batch processing, I found that my CPU utilization is also relatively low, and the time is also relatively long, especially the "recon-all" step. May I ask how to efficiently use the CPU core and shorten the time of data preprocessing?

glasserm commented 1 week ago

I think the next FreeSurfer will help with this. The question will be whether it also fixes the issues with surface placement that were in FS 7.

mharms commented 1 week ago

If you have multiple sessions to process, I suggest that you just run multiple sessions simultaneously – 1 core per session.

Cheers, -MH

-- Michael Harms, Ph.D.

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: @.***

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For fMRI, you can also remove global respiratory artifact using temporal ICA. For unstructured noise, we recommend parcellation. We are working on other methods for non-parcellated analyses, but have not yet published detailed guidelines on that.

Hello, I have a question the CPU of my personal computer is 20 cores and 28 threads. During batch processing, I found that my CPU utilization is also relatively low, and the time is also relatively long, especially the "recon-all" step. May I ask how to efficiently use the CPU core and shorten the time of data preprocessing?

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RuiWang0805 commented 3 days ago

I think the next FreeSurfer will help with this. The question will be whether it also fixes the issues with surface placement that were in FS 7.

Hi, when I run the GenericfMRISurfaceProcessingPipeline steps, I found that the amount of time special long, eg more than 23 h, but also in the running, I use slrum scheduling software runs seven subjects, Before GenericfMRISurfaceProcessingPipeline previous steps to run a successful and running time is similar

glasserm commented 3 days ago

How are you calling the pipeline? That one should be fairly fast.

RuiWang0805 commented 3 days ago

How are you calling the pipeline? That one should be fairly fast.

This is a patient subject login cost long time:

Sat Nov 23 23:24:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Sat Nov 23 23:24:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Sat Nov 23 23:24:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0039
Sat Nov 23 23:24:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_RL
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.7.0-MOD-dd843a0a
     COMMIT: dd843a0a0294b699e29ea9618eb0c940c8d01f1d
   MODIFIED: YES
========================================
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Sat Nov 23 23:24:28 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Sat Nov 23 23:24:29 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/RibbonVolumeToSurfaceMapping
Sat Nov 23 23:24:29 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sat Nov 23 23:24:29 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sat Nov 23 23:24:29 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.466924
0.982023
.7485610
1.2154850
Sat Nov 23 23:30:02 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Sat Nov 23 23:30:02 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Sat Nov 23 23:30:02 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sat Nov 23 23:30:02 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sat Nov 23 23:30:02 CST 2024:SurfaceSmoothing.sh: START
Sat Nov 23 23:30:27 CST 2024:SurfaceSmoothing.sh: END
Sat Nov 23 23:30:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: START
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/ROIs
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_RL
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Sat Nov 23 23:30:27 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Sat Nov 23 23:30:33 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Sat Nov 23 23:31:01 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Sat Nov 23 23:31:01 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Sun Nov 24 03:16:58 CST 2024:SubcorticalProcessing.sh: END
Sun Nov 24 03:16:58 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Sun Nov 24 03:16:58 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 03:16:59 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 03:16:59 CST 2024:CreateDenseTimeseries.sh: START
Sun Nov 24 03:17:06 CST 2024:CreateDenseTimeseries.sh: END
Sun Nov 24 03:17:06 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: Subject: 0039
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_RL
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Sun Nov 24 03:17:06 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Sun Nov 24 03:17:22 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_LR --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0039
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_LR
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Sun Nov 24 03:17:22 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.7.0-MOD-dd843a0a
     COMMIT: dd843a0a0294b699e29ea9618eb0c940c8d01f1d
   MODIFIED: YES
========================================
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Sun Nov 24 03:17:23 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/RibbonVolumeToSurfaceMapping
Sun Nov 24 03:17:23 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 03:17:23 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 03:17:23 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.469014
0.983727
.7492200
1.2182340
Sun Nov 24 03:22:39 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Sun Nov 24 03:22:39 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Sun Nov 24 03:22:39 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 03:22:39 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 03:22:39 CST 2024:SurfaceSmoothing.sh: START
Sun Nov 24 03:23:02 CST 2024:SurfaceSmoothing.sh: END
Sun Nov 24 03:23:02 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: START
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/ROIs
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_LR
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Sun Nov 24 03:23:02 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Sun Nov 24 03:23:07 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Sun Nov 24 03:23:32 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Sun Nov 24 03:23:32 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Sun Nov 24 07:05:09 CST 2024:SubcorticalProcessing.sh: END
Sun Nov 24 07:05:09 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Sun Nov 24 07:05:09 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sun Nov 24 07:05:09 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sun Nov 24 07:05:09 CST 2024:CreateDenseTimeseries.sh: START
Sun Nov 24 07:05:17 CST 2024:CreateDenseTimeseries.sh: END
Sun Nov 24 07:05:17 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_LR --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: Subject: 0039
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_LR
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Sun Nov 24 07:05:17 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Sun Nov 24 07:05:35 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Sun Nov 24 07:05:35 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!
glasserm commented 3 days ago

How long is the fMRI?

RuiWang0805 commented 3 days ago

rfMRI_REST1_RL

The step of rfMRI_REST1_RL cost more than 4hours and the step of rfMRI_REST1_LR also cost more than 4hours.

glasserm commented 3 days ago

How many timepoints?

RuiWang0805 commented 3 days ago

How many timepoints?

415

glasserm commented 3 days ago

That should be very fast. Are you having issues with thread contention?

RuiWang0805 commented 3 days ago

That should be very fast. Are you having issues with thread contention?

There should be no problem, when running the Genetic Volume step, the time is normal, I do not know why it takes so long to run the Genetic Surface step

glasserm commented 3 days ago

fMRISurface is nearly entirely multi-threaded. If you try to run multiple of them in parallel without some kind of thread control, it could cause a large amount of thread contention and slow things down a lot.

RuiWang0805 commented 3 days ago

fMRISurface is nearly entirely multi-threaded. If you try to run multiple of them in parallel without some kind of thread control, it could cause a large amount of thread contention and slow things down a lot.

I I'm not quite sure if my setup is correct, thanks for your reply！ ![Uploading Screenshot_2024-11-24-22-36-02-816_com.oray.sunlogin-edit.jpg…]()

RuiWang0805 commented 2 days ago

fMRISurface is nearly entirely multi-threaded. If you try to run multiple of them in parallel without some kind of thread control, it could cause a large amount of thread contention and slow things down a lot.

Smoothing and resampling run for a long time, I guess wb_command lacks dependencies?

coalsont commented 1 day ago

The volume predilate amount could be reduced, as noted in the comment (its purpose is to reduce ringing effects from cubic resampling, but -cifti-resample uses the average value of the edge to fill the background (instead of 0), and has for a while, so this is less of a concern than with 1.4.0). I'm not sure if that would make it take 4 hours on 2mm data, though. What version of workbench are you using?

coalsont commented 1 day ago

A mock test (91k file resampled to its own space) takes 10 minutes on 4 physical cores with the current 10mm predilate on a 1000 timepoint 2mm file. The smoothing step shouldn't take as long.

Are you using a multi-socket machine? Those have more overhead for thread synchronization when all cores are used, it is generally best to restrict each process to a single socket so that thread synchronization is fast. For a quick and dirty method, you can export OMP_NUM_THREADS=10 (or however many physical cores one socket has) and the OS scheduler will usually keep them all on one socket (depending on the cpu usage of other things you are running). I don't know what the best strategy is for the newer asymmetric "efficiency cores" processors, but if that is what you have, maybe restrict to the number of performance cores (single socket, if applicable) you have and see what happens.

RuiWang0805 commented 1 day ago

The volume predilate amount could be reduced, as noted in the comment (its purpose is to reduce ringing effects from cubic resampling, but -cifti-resample uses the average value of the edge to fill the background (instead of 0), and has for a while, so this is less of a concern than with 1.4.0). I'm not sure if that would make it take 4 hours on 2mm data, though. What version of workbench are you using?

Hi, My workbench version is ,2.0.1 -cifti-resample cost a long time: From Nov 22 21:52:52 to Nov 23 13:21:27 

[Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0039
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_RL
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.7.0-MOD-dd843a0a
     COMMIT: dd843a0a0294b699e29ea9618eb0c940c8d01f1d
   MODIFIED: no
========================================
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Fri Nov 22 21:52:52 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/RibbonVolumeToSurfaceMapping
Fri Nov 22 21:52:52 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Fri Nov 22 21:52:52 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Fri Nov 22 21:52:52 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.466924
0.982023
.7485610
1.2154850
Fri Nov 22 22:05:26 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Fri Nov 22 22:05:26 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Fri Nov 22 22:05:26 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Fri Nov 22 22:05:26 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Fri Nov 22 22:05:27 CST 2024:SurfaceSmoothing.sh: START
Fri Nov 22 22:06:39 CST 2024:SurfaceSmoothing.sh: END
Fri Nov 22 22:06:39 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: START
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/ROIs
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_RL
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Fri Nov 22 22:06:39 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Fri Nov 22 22:06:45 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Fri Nov 22 22:08:29 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Fri Nov 22 22:08:30 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Sat Nov 23 13:20:51 CST 2024:SubcorticalProcessing.sh: END
Sat Nov 23 13:20:51 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Sat Nov 23 13:20:51 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Sat Nov 23 13:20:51 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Sat Nov 23 13:20:51 CST 2024:CreateDenseTimeseries.sh: START
Sat Nov 23 13:20:59 CST 2024:CreateDenseTimeseries.sh: END
Sat Nov 23 13:20:59 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Sat Nov 23 13:20:59 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Sat Nov 23 13:21:00 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Sat Nov 23 13:21:00 CST 2024:GenerateFMRIScenes.sh: Subject: 0039
Sat Nov 23 13:21:00 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_RL
Sat Nov 23 13:21:00 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Sat Nov 23 13:21:00 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Sat Nov 23 13:21:27 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Sat Nov 23 13:21:27 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!
RuiWang0805 commented 1 day ago

The volume predilate amount could be reduced, as noted in the comment (its purpose is to reduce ringing effects from cubic resampling, but -cifti-resample uses the average value of the edge to fill the background (instead of 0), and has for a while, so this is less of a concern than with 1.4.0). I'm not sure if that would make it take 4 hours on 2mm data, though. What version of workbench are you using?

The simulation test (v 2.0.0) only on the workbench took very little time, and the longer it took seemed to be the Workbench version.

Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_LR --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0029-2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_LR
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.8.0-c87affc6
     COMMIT: c87affc61033fe8c9d71db67603d8346f6962ae0
   MODIFIED: no
========================================
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/RibbonVolumeToSurfaceMapping
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.439457
0.986688
.7669595
1.2064165
Tue Nov 26 20:56:39 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Tue Nov 26 20:56:39 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: START
Tue Nov 26 20:56:48 CST 2024:SurfaceSmoothing.sh: END
Tue Nov 26 20:56:48 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: START
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/ROIs
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Tue Nov 26 20:56:54 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Tue Nov 26 20:56:55 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Tue Nov 26 20:56:56 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Tue Nov 26 20:58:30 CST 2024:SubcorticalProcessing.sh: END
Tue Nov 26 20:58:30 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: START
Tue Nov 26 20:58:38 CST 2024:CreateDenseTimeseries.sh: END
Tue Nov 26 20:58:38 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_LR --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: Subject: 0029-2
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_LR
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Tue Nov 26 20:58:54 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Tue Nov 26 20:58:54 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!
coalsont commented 19 hours ago

The test I ran was on the development branch of workbench, which should be effectively the same as 2.0.1. It looked like you initially wrote "version 1.2.3" and then edited it to 2.0.1. Version 1.2.3 was released in 2016, and the speed of dilation was substantially improved in v1.4.2 (in 2020). Can you clarify if you are seeing this slowness with workbench v2.0.1?

RuiWang0805 commented 15 hours ago

The test I ran was on the development branch of workbench, which should be effectively the same as 2.0.1. It looked like you initially wrote "version 1.2.3" and then edited it to 2.0.1. Version 1.2.3 was released in 2016, and the speed of dilation was substantially improved in v1.4.2 (in 2020). Can you clarify if you are seeing this slowness with workbench v2.0.1?

I used workbench"version "2.0.0" test to run one subject (without slrum scheduling software), as shown in 0029-2 (login1), the running time was relatively fast, about 12 minutes, and then I tested 8 subjects (slrum scheduling software). The time to run a subject (RL/LR) is relatively long, about 4-5h (login2), The process file ${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii this step is very slow (SubcorticalProcessing.sh line119), As can be seen from login2, the running time is very slow, and the CPU monitoring software can also see that the process has been stuck in the process file ${ResultsFolder}/${NameOffMRI}_temp_template.dlabel.nii step.

login1 run for patient 0029-2(RL):

Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_RL --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0029-2
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_RL
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.8.0-c87affc6
     COMMIT: c87affc61033fe8c9d71db67603d8346f6962ae0
   MODIFIED: no
========================================
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Tue Nov 26 20:45:56 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_RL/RibbonVolumeToSurfaceMapping
Tue Nov 26 20:45:56 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:45:56 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:45:56 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.436878
0.984503
.7660640
1.2029420
Tue Nov 26 20:50:12 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Tue Nov 26 20:50:12 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Tue Nov 26 20:50:12 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:50:12 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:50:12 CST 2024:SurfaceSmoothing.sh: START
Tue Nov 26 20:50:21 CST 2024:SurfaceSmoothing.sh: END
Tue Nov 26 20:50:21 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: START
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/ROIs
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_RL
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_RL
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Tue Nov 26 20:50:21 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Tue Nov 26 20:50:27 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Tue Nov 26 20:50:29 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Tue Nov 26 20:50:29 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Tue Nov 26 20:51:59 CST 2024:SubcorticalProcessing.sh: END
Tue Nov 26 20:51:59 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Tue Nov 26 20:51:59 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:51:59 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:51:59 CST 2024:CreateDenseTimeseries.sh: START
Tue Nov 26 20:52:06 CST 2024:CreateDenseTimeseries.sh: END
Tue Nov 26 20:52:06 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_RL --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: Subject: 0029-2
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_RL
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Tue Nov 26 20:52:06 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Tue Nov 26 20:52:24 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!

login1 run for patient 0029-2(LR):

Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_LR --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0029-2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_LR
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.8.0-c87affc6
     COMMIT: c87affc61033fe8c9d71db67603d8346f6962ae0
   MODIFIED: no
========================================
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Tue Nov 26 20:52:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/RibbonVolumeToSurfaceMapping
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:52:24 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.439457
0.986688
.7669595
1.2064165
Tue Nov 26 20:56:39 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Tue Nov 26 20:56:39 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:56:39 CST 2024:SurfaceSmoothing.sh: START
Tue Nov 26 20:56:48 CST 2024:SurfaceSmoothing.sh: END
Tue Nov 26 20:56:48 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: START
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/ROIs
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Tue Nov 26 20:56:48 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Tue Nov 26 20:56:54 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Tue Nov 26 20:56:55 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Tue Nov 26 20:56:56 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Tue Nov 26 20:58:30 CST 2024:SubcorticalProcessing.sh: END
Tue Nov 26 20:58:30 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 20:58:30 CST 2024:CreateDenseTimeseries.sh: START
Tue Nov 26 20:58:38 CST 2024:CreateDenseTimeseries.sh: END
Tue Nov 26 20:58:38 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0029-2 --fmriname=rfMRI_REST1_LR --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: Subject: 0029-2
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_LR
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0029-2/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Tue Nov 26 20:58:38 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Tue Nov 26 20:58:54 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Tue Nov 26 20:58:54 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!

login2 run for patient by using slrum scheduling software(RL):

Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0039
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_RL
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.8.0-c87affc6
     COMMIT: c87affc61033fe8c9d71db67603d8346f6962ae0
   MODIFIED: no
========================================
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Tue Nov 26 21:06:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/RibbonVolumeToSurfaceMapping
Tue Nov 26 21:06:16 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 21:06:16 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 21:06:16 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.466924
0.982023
.7485610
1.2154850
Tue Nov 26 21:15:43 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Tue Nov 26 21:15:43 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Tue Nov 26 21:15:43 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 21:15:43 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 21:15:44 CST 2024:SurfaceSmoothing.sh: START
Tue Nov 26 21:16:34 CST 2024:SurfaceSmoothing.sh: END
Tue Nov 26 21:16:34 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: START
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/ROIs
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_RL
Tue Nov 26 21:16:34 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Tue Nov 26 21:16:35 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Tue Nov 26 21:16:35 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL
Tue Nov 26 21:16:35 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Tue Nov 26 21:16:35 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Tue Nov 26 21:16:40 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Tue Nov 26 21:17:40 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Tue Nov 26 21:17:40 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Tue Nov 26 23:58:16 CST 2024:SubcorticalProcessing.sh: END
Tue Nov 26 23:58:16 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Tue Nov 26 23:58:16 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 23:58:16 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 23:58:16 CST 2024:CreateDenseTimeseries.sh: START
Tue Nov 26 23:58:24 CST 2024:CreateDenseTimeseries.sh: END
Tue Nov 26 23:58:24 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_RL --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: Subject: 0039
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_RL
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_RL/fMRIQC
Tue Nov 26 23:58:24 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Tue Nov 26 23:58:44 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Tue Nov 26 23:58:44 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!

login2 run for patient by using slrum scheduling software(LR):

Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: arguments: --path=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_LR --lowresmesh=32 --fmrires=2 --smoothingFWHM=2 --grayordinatesres=2 --regname=MSMSulc
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Path: /home/ruiwang1997/projects/Pipelines_ExampleData
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subject: 0039
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: NameOffMRI: rfMRI_REST1_LR
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: LowResMesh: 32
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FinalfMRIResolution: 2
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: SmoothingFWHM: 2
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: GrayordinatesResolution: 2
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: RegName: MSMSulc
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: QCMode: YES
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: doGoodVoxels: YES
========================================
  DIRECTORY: /home/ruiwang1997/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: Post-v4.8.0-c87affc6
     COMMIT: c87affc61033fe8c9d71db67603d8346f6962ae0
   MODIFIED: no
========================================
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: FSLDIR: /usr/local/fsl
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Platform Information Follows: 
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Make fMRI Ribbon
Tue Nov 26 23:58:45 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: mkdir -p /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/RibbonVolumeToSurfaceMapping
Tue Nov 26 23:58:45 CST 2024:RibbonVolumeToSurfaceMapping.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Tue Nov 26 23:58:45 CST 2024:RibbonVolumeToSurfaceMapping.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Tue Nov 26 23:58:45 CST 2024:RibbonVolumeToSurfaceMapping.sh: START
0.469014
0.983727
.7492200
1.2182340
Wed Nov 27 00:06:48 CST 2024:RibbonVolumeToSurfaceMapping.sh: END
Wed Nov 27 00:06:48 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Surface Smoothing
Wed Nov 27 00:06:48 CST 2024:SurfaceSmoothing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Wed Nov 27 00:06:48 CST 2024:SurfaceSmoothing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Wed Nov 27 00:06:48 CST 2024:SurfaceSmoothing.sh: START
Wed Nov 27 00:07:36 CST 2024:SurfaceSmoothing.sh: END
Wed Nov 27 00:07:36 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Subcortical Processing
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: START
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: AtlasSpaceFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: ROIFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/ROIs
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: FinalfMRIResolution: 2
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: ResultsFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: NameOffMRI: rfMRI_REST1_LR
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: SmoothingFWHM: 2
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: BrainOrdinatesResolution: 2
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: VolumefMRI: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: Sigma: .84932180028801904272
Wed Nov 27 00:07:36 CST 2024:SubcorticalProcessing.sh: Creating subject-roi subcortical cifti at same resolution as output
Wed Nov 27 00:07:41 CST 2024:SubcorticalProcessing.sh: Dilating out zeros
Wed Nov 27 00:08:43 CST 2024:SubcorticalProcessing.sh: Generate atlas subcortical template cifti
Wed Nov 27 00:08:44 CST 2024:SubcorticalProcessing.sh: Smoothing and resampling
Wed Nov 27 02:09:09 CST 2024:SubcorticalProcessing.sh: END
Wed Nov 27 02:09:09 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generation of Dense Timeseries
Wed Nov 27 02:09:09 CST 2024:CreateDenseTimeseries.sh: HCPPIPEDIR: /home/ruiwang1997/HCPpipelines
Wed Nov 27 02:09:09 CST 2024:CreateDenseTimeseries.sh: CARET7DIR: /home/ruiwang1997/HCPpipelines/workbench/bin_linux64
Wed Nov 27 02:09:09 CST 2024:CreateDenseTimeseries.sh: START
Wed Nov 27 02:09:17 CST 2024:CreateDenseTimeseries.sh: END
Wed Nov 27 02:09:17 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Generating fMRI QC scene and snapshots
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: arguments: --study-folder=/home/ruiwang1997/projects/Pipelines_ExampleData --subject=0039 --fmriname=rfMRI_REST1_LR --output-folder=/home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: StudyFolder: /home/ruiwang1997/projects/Pipelines_ExampleData
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: Subject: 0039
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: fMRIName: rfMRI_REST1_LR
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: OutputSceneFolder: /home/ruiwang1997/projects/Pipelines_ExampleData/0039/MNINonLinear/Results/rfMRI_REST1_LR/fMRIQC
Wed Nov 27 02:09:17 CST 2024:GenerateFMRIScenes.sh: verboseArg: false
Wed Nov 27 02:09:35 CST 2024:GenerateFMRIScenes.sh: fMRI QC scene generation completed
Wed Nov 27 02:09:35 CST 2024:GenericfMRISurfaceProcessingPipeline.sh: Completed!
coalsont commented 12 hours ago

Try adding --export=OMP_NUM_THREADS=4 to your sbatch command and see what the timing looks like then. If it improves things, then perhaps the slurm setup should do something to improve the default behavior of multithreading. I believe we use cpusets on our CHPC cluster to basically split the multi-socket machines into two logical nodes. We have also seen some odd results from high core count single-socket systems. As long as you aren't hitting memory limits, keeping the threading lower and running many subjects per node may be more throughput-efficient, if you have enough subjects to saturate the nodes.