[nrrd] nrrdLoad: trouble reading .nii.gz --> UKFTractography in pnlpipe docker container

[kavandeloo97]

Hi there, I get an error when trying to run UKFTractography in the pnlpipe docker container (please advise, thank you in advance!):

(pnlpipe3) [root@156c1c951699 dwi]# UKFTractography --dwiFile sub-HV153_ses-01_desc-UnXc_dwi_EdEp.nii.gz --maskFile sub-HV153_ses-01_desc-UnXc_dwi_maskQc.nii.gz --numThreads 8 --seedsPerVoxel 5 --recordTensors --freeWater --recordFreeWater --tracts ./sub-HV153_ses-01_desc-UnXc_dwi_EdEp.vtk

Using the 2T simple model with free water estimation. Setting the default parameters accordingly:
"*": set by user
"-": default setting

• stoppingFA: 0.15

• seedingThreshold: 0.18

• Qm: 0.001
• Ql: 50
• Rs: 0.02

• stepLength: 0.3
• recordLength: 0.9

• Qw: 0.0015

• stoppingThreshold: 0.1
• seedsPerVoxel: 5
  Found 8 cores on your system.
  Running tractography with 8 thread(s).
  Trouble reading sub-HV153_ses-01_desc-UnXc_dwi_EdEp.nii.gz: [nrrd] nrrdLoad: trouble reading "sub-HV153_ses-01_desc-UnXc_dwi_EdEp.nii.gz"
  [nrrd] nrrdRead: trouble
  [nrrd] _nrrdRead: couldn't parse "|q{B,$X!*`wzfgw{[U;;sYwgg" as magic or beginning of any recognized format

ISignalData could not be loaded
UKFTractography: ITK ExceptionObject caught!

itk::ExceptionObject (0x55d24ad8a9e0)
Location: "unknown"
File: /home/pnlbwh/pnlpipe/soft_dir/ukftractography/UKFTractography/UKFTractography.cxx
Line: 70
Description: itk::ERROR: ::LoadFiles failed with unknown error.

[tashrifbillah]

Hi Katie, it works with nrrd format only. Use nhdr_write.py to write an associated nhdr file and provide --dwiFile sub-HV153_ses-01_desc-UnXc_dwi_EdEp.nhdr