Tractoflow 2.4.3 under Debian 12 (versus CentOS 7.5)

1

I just tried running tractoflow using the singularity container (scilus_1.6.0.sif) under Debian 12, but got a couple of errors fairly early in the pipeline. I’m running nextflow v21.10.6.

Tractoflow, with the same anaconda3 installation, environment, singularity version, etc., works perfectly under CentOS 7.5

Under Debian 12, tractflow starts okay, runs through BIDS checks but when it gets to DWI_denoise, some time after starting to run dwidnoise, I get the following error


dwidenoise: [100%] uncompressing image "sub-S5673YAM_dir-RL_dwi.nii.gz"
dwidenoise: [100%] preloading data for "sub-S5673YAM_dir-RL_dwi.nii.gz"
dwidenoise: [100%] running MP-PCA denoising
dwidenoise: [100%] compressing image "dwi_denoised.nii.gz"
terminate called after throwing an instance of 'NiftiIO::NiftiException'
  what():  Error: short write, output file will be truncated
/fsl/share/fsl/bin/fslmaths: line 2: 2138930 Aborted                 /fsl/bin/fslmaths "$@"

And then another error later (during brain extraction or N4 correction?) …

   Using antsBrainExtraction with the following arguments:
      image dimension         = 3
      anatomical image        = sub-S5673YAM__t1_resampled.nii.gz
      extraction template     = /human-data/mni_152_sym_09c/t1/t1_template.nii.gz
      extraction reg. mask    = 
      extraction prior        = /human-data/mni_152_sym_09c/t1/t1_brain_probability_map.nii.gz
      output prefix           = bet/
      output image suffix     = nii.gz

    N4 parameters (pre brain extraction):
      convergence             = [ 50x50x50x50,0.0000001 ]
      shrink factor           = 4
      B-spline parameters     = [ 200 ]

    Atropos parameters (extraction):
       convergence            = [ 3,0.0 ]
       likelihood             = Gaussian
       initialization         = kmeans[ 3 ]
       mrf                    = [ 0.1,1x1x1 ]
       use clock random seed  = 0

** ERROR: NWAD: wrote only 0 of 46923776 bytes to file
Exception caught during reference file reading 

itk::ImageFileReaderException (0x5570ef2376c0)
Location: "unknown" 
File: /ants_build/staging/include/ITK-5.3/itkImageFileReader.hxx
Line: 132
Description:  Could not create IO object for reading file bet/N4Corrected0.nii.gz
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

 file bet/N4Corrected0.nii.gz
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /ants_build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1339:
ITK ERROR: LaplacianRecursiveGaussianImageFilter(0x5570ef2316e0): Input Primary is required but not set.
/ants/bin/antsBrainExtraction.sh: line 123: 2122265 Aborted                 ( "$@" )

Anyone using tractoflow under Debian 12 successfully?

Thanks,
Chris

2

This issue is not yet resolved. I re-downloaded the most recent singularity container, scilus_1.6.0.sif (and it does work on the Debian 12 system.

I had been using a slightly older version of scilus_1.6.0.sif (Oct vs Dec 2023).

image
image1041×401 16.3 KB

3

Problem is back. Same issue as before.

dwidenoise: [100%] compressing image "dwi_denoised.nii.gz"
terminate called after throwing an instance of 'NiftiIO::NiftiException'
  what():  Error: short write, output file will be truncated
/fsl/share/fsl/bin/fslmaths: line 2: 2138930 Aborted
4

Hi @Chyatt,

Is it specific to fsl commands ?
Can you try running a fsl command outside of nextflow, using singularity exec ?
Please provide the command you run as well as the output it gives you.

Thank you in advance
Arnaud

5

HI @abore

I ran the following on the Debian 12 system ($SING is an env variable - the path to scilus_1.6.0.sif).

singularity exec $SING fslmaths sub-S5673YAM_T1w.nii.gz -add 0 test

Image Exception : #63 :: No image files match: sub-S5673YAM_T1w
terminate called after throwing an instance of 'std::runtime_error'
  what():  No image files match: sub-S5673YAM_T1w
/fsl/share/fsl/bin/fslmaths: line 2: 3516524 Aborted                 /fsl/bin/fslmaths "$@"

It looks like it’s not recognizing the .nii.gz extension.

I tried the exact same command under CentOS 7.5 and it ran okay and produced the test.nii.gz output file.

Also should note:
Under CentOS 7.5 we are using singularity version 3.5.3-1.1.el7
Under Debian 12 we are using singularity-ce version 4.1.2-jammy

Thank you,
Chris