example file Pos_b0 missing

[Ralf Veit]

Dear HCP-Users

I’m currently testing the HCP pipeline for diffusion preprocessing with the example data set for 100307. We intend to use to pipeline for our own dataset. The Pre_Freesurfer, the Freesurfer and the Post_Freesurfer processing pipeline went through without any problems.  When running the DiffusionPreprocessingBatch.sh script, I received the following error

Image Exception : #63 :: No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

However, when I look in the folder …/diffusion/topup/ there is a file Pos_b0.nii.gz. A closer inspection revealed that already during basic_preproc_norm_intensity the Pos1_mean was not created, as well as all files with fsl_roi were not created (and subsequent files). I checked the script basic_preproc_norm_intensity.sh and saw that there should be an error message when this mean image cannot be created, but there was no error message. basic_preproc_norm_intensity.sh: Processing /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/rawdata/Pos_1

basic_preproc_norm_intensity.sh: About to fslmaths /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/rawdata/Pos_1.nii.gz -Xmean -Ymean -Zmean /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/rawdata/Pos_1_mean

Interestingly, I can run the command without problems at the console and the Pos_1_mean file will be created.

Any ideas what went wrong?

 

Best

Ralf

[Glasser, Matt]

How did you call the diffusion preprocessing pipeline?  What version of FSL are you using?

Matt.

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[Ralf Veit]

Dear Matt

I call the script ./DiffusionPreProcessingBatch.sh in the folder HCPpipelines-master/Examples/Scripts and modified only the Subjlist, the StudyFolder and the path for the Environment script.

I realized that the FSL version has an influence on data processing. I tried three different version of fsl. Using fsl-6, the script immediately crashes with the following error message /opt_prg/fsl/fsl-6/bin/fslhd: error while loading shared libraries: libopenblas.so.0:

With fsl 6.0.4 I got the following error message

Image Exception : #63 :: No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 166: % 2: syntax error: operand expected (error token is "% 2")

/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 480: [: -eq: unary operator expected

With fsl 6.0.6.2, the script produces more files, but also more error messages

  Image Exception : #63 :: No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 166: % 2: syntax error: operand expected (error token is "% 2")

/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 480: [: -eq: unary operator expected

cat: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/rawdata/Pos_1_b0_0000.bval: No such file or directory

cat: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/rawdata/Pos_1_b0_0000.bval: No such file or directory

Mon Mar 13 17:12:17 CET 2023:basic_preproc_sequence.sh: While running '/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/scripts/basic_preproc_sequence.sh /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion .111540 1 45 50':

Mon Mar 13 17:12:17 CET 2023:basic_preproc_sequence.sh: ERROR: 'Posbvals=' command failed with return code: 1

I attached the two logfiles for the different fsl versions and also a file with the data tree in the raw data folder.

Best

Ralf

[Ralf Veit]

Just one more info regrading the files in the topup folder using different fsl version

topup folder
fsl6.0.4
|-- acqparams.txt
|-- extractedb0.txt
|-- Neg_b0.nii.gz
|-- Pos_b0.nii.gz
`-- Pos_Neg_b0.nii.gz

fsl6.0.6.2
no files

[Tim Coalson]

Several of those errors result from the first error, which is "fslval <...>/Pos_b0 dim3" failing.  Have you tried running that fslval manually?  If it works, there must be some kind of environment difference between your terminal and how the pipeline gets launched (effective user ID?).

Tim

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[Glasser, Matt]

Perhaps this is also related to this recent FSL bug (and then the other versions have things like library errors)?

Matt.

[Jure Demsar]

Hi,

1. This error can be ignored:

/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 166: % 2: syntax error: operand expected (error token is "% 2")
/opt_prg/spm_tool_12/HCPpipelines-master/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh: line 480: [: -eq: unary operator expected

It is just a malfunctioning safety check. If you remember we already fixed it at some locations, it seems like we somehow missed the one in this script. The error is that the input variable to the isodd function is not set.

2. Regarding the other bug, I think Tim might be correct here, it seems like one of the previous steps is failing and there is no Pos_b0 file in the topup folder. Ralf, are you using the latest version of the HCP Pipelines (the current tip of the master branch)?

Jure

[Jure Demsar]

As a sanity check, I ran the diffusion pipeline on one of my test sessions using the latest master of HCP Pipelines and FSL 6.0.6.2 and the processing is already past the point where in crashed in the attached log. So this seems like an environment issue.

[Ralf Veit]

Dear all,

thank your for your suggestions. I downloaded the recent HCPpipeline and rerun the analyses with slightly progress. Unfortunately, the output logfile shows:

Image Exception : #63 :: No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0
No image files match: /server/fo2-17/data/Ralf/projects/Pipelines_ExampleData/100307/Diffusion/topup/Pos_b0

However, there is a file Pos_b0.nii.gz in the topup folder. Later, comes the following message: Topup::topup_clp::topup_clp: Subsampling levels incompatible with image data.
I attached, once again the two log files. Do you have any idea which enviroment variables I should change that the script is running?

fsl was downloaded for centos7, while the script runs on a machine with Rocky Linux 9.1 (due to GNU).  

Best
Ralf

[Glasser, Matt]

Looks like you are affected by an eddy_quad bug.  I think someone else on the list was affected and resolved it by updating FSL or getting a fixed eddy_quad directly from the Oxford folks.

[Jure Demsar]

There is a quick fix for this in https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/7ewa-Wxp-kM.