Hi @mattcieslak,

Three things:

1. Following on from #400, it appears that omitting the --output-space and --output-resolution when running reconstruction workflows produces the ODF plots in the HTML file. I've confirmed with both the AMICO NODDI work flow and the SS3T workflow.

2. It used to be that the tractography-based workflow HTML reports had plots for the ROI-to-ROI connectivity for each atlas. Has that behavior changed because, for the SS3T reconstruction, I'm only getting ODF plots or is this a consequence of not having the flags for the output space? I don't specifically care either way, just making sure I haven't unintentionally broken something else by excluding flags.

3. Likewise, it used to be that the co-registered atlases were saved to the output folder. Right now, I appear to get relevant files except for the specific atlas spaces (they are still in the --work directory). As long as this is working as intended, I'm good. Here's the outputs from the workflow in dwi/:

sub-971_space-T1w_desc-preproc_desc-csfFOD_ss3tcsd.txt
sub-971_space-T1w_desc-preproc_desc-csfFODmtnormed_ss3tcsd.mif.gz
sub-971_space-T1w_desc-preproc_desc-gmFOD_ss3tcsd.txt
sub-971_space-T1w_desc-preproc_desc-gmFODmtnormed_ss3tcsd.mif.gz
sub-971_space-T1w_desc-preproc_desc-mtinliermask_ss3tcsd.nii.gz
sub-971_space-T1w_desc-preproc_desc-mtnorm_ss3tcsd.nii.gz
sub-971_space-T1w_desc-preproc_desc-siftweights_ifod2.csv
sub-971_space-T1w_desc-preproc_desc-tracks_ifod2.tck
sub-971_space-T1w_desc-preproc_desc-wmFOD_ss3tcsd.txt
sub-971_space-T1w_desc-preproc_desc-wmFODmtnormed_ss3tcsd.mif.gz
sub-971_space-T1w_desc-preproc_dhollanderconnectome.mat

Hi there,

I was trying out qsiprep v0.14.2 and I encountered this error when it tries to run eddy_openmp

EDDY:::  ECScanManager::GetGlobal2DWIIndexMapping: Global index not dwi
EDDY:::  ECScanClasses.cpp:::  unsigned int EDDY::ECScanManager::GetGlobal2DWIIndexMapping(unsigned int) const:  Exception thrown
EDDY:::  ECScanClasses.h:::  void EDDY::ECScanManager::ApplyDWILocationReference():  Exception thrown
EDDY::: Eddy failed with message EDDY:::  eddy.cpp:::  EDDY::ReplacementManager* EDDY::DoVolumeToVolumeRegistration(const EDDY::EddyCommandLineOptions&, EDDY::E
CScanManager&):  Exception thrown

It is already using the --data_is_shelled flag. I'm not quite sure what is causing this issue. The closest thing that I could find was this thread (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;551b44e1.2002) where it says that there may be a programming bug in fsl. Is that the case here?

For some weird reason we can run eddy just fine on our data with fsl 6.0.4 if we call it directly.

Would appreciate any help on this!

Best Regards, Bing Cai

Adds Patch2Self

Hi Everyone,

This PR adds the basic version of our method: Patch2Self: Denoising Diffusion MRI with Self-supervised Learning

The paper was published in NeurIPS 2020. Link: Paper

• [x] Make Interface via DIPY (added to dipy.py)
• [x] Add to workflows
• [x] Add tests

@mattcieslak Does this look okay? Let me know if I missed something! Where would this workflow ideally go?

Hi,

This bug might be more related to FSL. But I will post it here anyway.

When running qsiprep v.0.11.0 using eddy_cuda with the flag --estimate_move_by_susceptibility. Our group get the following error:

Related to the dataset from #98, I get the following when concatenating (ses-bline shown but ses-ptx has the same error reported):

Node: qsiprep_wf.single_subject_allo103_wf.dwi_preproc_ses_bline_acq_b_wf.pre_hmc_wf.merge_and_denoise_wf.dwi_qc_wf.concat_raw_dwis
Working directory: /data/allo/derivatives/qsiprep-0.8.0RC2/test/scratch/qsiprep_wf/single_subject_allo103_wf/dwi_preproc_ses_bline_acq_b_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/concat_raw_dwis

Node inputs:

compress = True
dtype = f4
header_source = <undefined>
in_files = ['/nifti/sub-allo103/ses-bline/dwi/sub-allo103_ses-bline_acq-b1000_dir-PA_run-001_dwi.nii.gz', '/nifti/sub-allo103/ses-bline/dwi/sub-allo103_ses-bline_acq-b2000_dir-PA_run-001_dwi.nii.gz']
is_dwi = True

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/nilearn.py", line 133, in _run_interface
    new_nii = concat_imgs(self.inputs.in_files, dtype=self.inputs.dtype)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 459, in concat_niimgs
    memory=memory, memory_level=memory_level))):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 150, in _iter_check_niimg
    niimg.shape))
ValueError: Field of view of image #1 is different from reference FOV.
Reference affine:
array([[ -0.85939997,   0.        ,  -0.        , 106.85299683],
       [ -0.        ,   0.85939997,  -0.        , -87.10998535],
       [  0.        ,   0.        ,   3.        , -91.61499786],
       [  0.        ,   0.        ,   0.        ,   1.        ]])
Image affine:
array([[ -0.85939997,   0.        ,  -0.        , 109.56999969],
       [ -0.        ,   0.85939997,  -0.        , -86.47598267],
       [  0.        ,   0.        ,   3.        , -92.52089691],
       [  0.        ,   0.        ,   0.        ,   1.        ]])
Reference shape:
(256, 256, 50)
Image shape:
(256, 256, 50, 21)

mrinfo on the dwis:

************************************************
Image:               "sub-allo103_ses-bline_acq-b1000_dir-PA_run-001_dwi.nii.gz"
************************************************
  Dimensions:        256 x 256 x 50 x 26
  Voxel size:        0.8594 x 0.8594 x 3 x 14
  Data strides:      [ -1 2 3 4 ]
  Format:            NIfTI-1.1 (GZip compressed)
  Data type:         signed 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1           0          -0      -112.3
                                0           1          -0      -87.11
                               -0           0           1      -91.61
  comments:          TE=87;Time=164022.000
************************************************
Image:               "sub-allo103_ses-bline_acq-b2000_dir-PA_run-001_dwi.nii.gz"
************************************************
  Dimensions:        256 x 256 x 50 x 21
  Voxel size:        0.8594 x 0.8594 x 3 x 17
  Data strides:      [ -1 2 3 4 ]
  Format:            NIfTI-1.1 (GZip compressed)
  Data type:         signed 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1           0          -0      -109.6
                                0           1          -0      -86.48
                               -0           0           1      -92.52
  comments:          TE=99;Time=164858.000

Hi @mattcieslak,

I got the following crash report when running qsiprep 0.14.2 for dsi data collected with two runs and a fieldmap:

Node: qsiprep_wf.single_subject_BR371_wf.dwi_preproc_ses_1_dir_AP_wf.confounds_wf.concat Working directory: /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/concat

Node inputs:

denoising_confounds = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged_confounds.csv fd = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/fdisp/fd_power_2012.txt motion = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/add_motion_headers/eddy_correctedspm_rp_motion.tsv original_bvals = ['/tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged.bval'] original_bvecs = ['/tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged.bvec'] original_files = ['/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz', '/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz'] sliceqc_file = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_outlier_n_sqr_stdev_map

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 428, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py", line 61, in _run_interface newpath=runtime.cwd, File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py", line 171, in _gather_confounds raise Exception("Gradients or original files don't match. File a bug report!") Exception: Gradients or original files don't match. File a bug report!

This is the command I used to run qsiprep: #Run qsiprep qsiprep-docker $bids_root_dir $bids_root_dir/derivatives \ participant \ --participant-label $subj \ --skip_bids_validation \ --fs-license-file $HOME/BRAINY_BIDS/derivatives/license.txt \ --output-resolution 1.2 \ --nthreads $nthreads \ --stop-on-first-crash \ --mem_mb $mem_mb

Please let me know your thoughts on how best to proceed, thank you!

Hi @mattcieslak, Ran the preprocessing steps and got the following error. It looks like it kept running after the error and wrote all the files except the figures and report.

 Node: qsiprep_wf.single_subject_omega033_wf.dwi_preproc_ses_bline_dir_AP_run_001_wf.hmc_sdc_wf.pre_topup_enhance.n4_correct
Working directory: /data/omega/derivatives/qsiprep-0.6.4/baseline_2mm-iso_dedicated-fmap/scratch/qsiprep_wf/single_subject_omega033_wf/dwi_preproc_ses_bline_dir_AP_run_001_wf/hmc_sdc_wf/pre_topup_enhance/n4_correct

Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = 150.0
bspline_order = 3
convergence_threshold = 1e-06
copy_header = True
dimension = 3
environ = {'NSLOTS': '1'}
input_image = /data/omega/derivatives/qsiprep-0.6.4/baseline_2mm-iso_dedicated-fmap/scratch/qsiprep_wf/single_subject_omega033_wf/dwi_preproc_ses_bline_dir_AP_run_001_wf/hmc_sdc_wf/pre_topup_enhance/rescale_image/vol0000_LPS_TruncateImageIntensity_RescaleImage.nii.gz
mask_image = <undefined>
n_iterations = [200, 200]
num_threads = 1
output_image = <undefined>
save_bias = False
shrink_factor = <undefined>
weight_image = /data/omega/derivatives/qsiprep-0.6.4/baseline_2mm-iso_dedicated-fmap/scratch/qsiprep_wf/single_subject_omega033_wf/dwi_preproc_ses_bline_dir_AP_run_001_wf/hmc_sdc_wf/pre_topup_enhance/smooth_mask/vol0000_LPS_TruncateImageIntensity_RescaleImage_mask_FillHoles_MD_G.nii.gz

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/ants/segmentation.py", line 438, in _run_interface
    runtime, correct_return_codes)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
N4BiasFieldCorrection --bspline-fitting [ 150, 3 ] -d 3 --input-image /data/omega/derivatives/qsiprep-0.6.4/baseline_2mm-iso_dedicated-fmap/scratch/qsiprep_wf/single_subject_omega033_wf/dwi_preproc_ses_bline_dir_AP_run_001_wf/hmc_sdc_wf/pre_topup_enhance/rescale_image/vol0000_LPS_TruncateImageIntensity_RescaleImage.nii.gz --convergence [ 200x200, 1e-06 ] --output vol0000_LPS_TruncateImageIntensity_RescaleImage_corrected.nii.gz --weight-image /data/omega/derivatives/qsiprep-0.6.4/baseline_2mm-iso_dedicated-fmap/scratch/qsiprep_wf/single_subject_omega033_wf/dwi_preproc_ses_bline_dir_AP_run_001_wf/hmc_sdc_wf/pre_topup_enhance/smooth_mask/vol0000_LPS_TruncateImageIntensity_RescaleImage_mask_FillHoles_MD_G.nii.gz
Standard output:

Standard error:

Return code: 1

Problem or no?

I have a dataset that has full dwi scans in both AP and PA directions. My understanding is that I should be including the --distortion-group-merge average option in command line, per the "Preprocessing HCP-style" section. The documentation here suggests I should be including the --combine-all-dwis option as well, but I believe that flag has been removed (and is the default option?).

However, in terms of setting up the BIDS-valid dataset, am I right in thinking that I should put both of these scans (AP and PA) in the dwi folder? Also, is there any metadata field that needs to be added? I have tried a couple different options but kept running into errors.

Thanks, Andrew

Dear @mattcieslak, we are running an analysis in which we're aligning streamline endpoints to native space surface vertices. There seemed to be some issue of misalignment and I think we've traced it back to the qsiprep preprocessed T1w images.

Below are data from HCP subject 105923. The first screenshot is the native freesurfer pial surface (after hcp preprocessing) overlaid on the T1w_acpc_dc_restore.nii image found in the HCP minimally preprocessed download. Looks good:

The below screenshot is the same surface segmentation overlaid on the qsiprep preprocessed T1w image from HCP unprocessed data. Here was the command I used:

qsiprep-docker \
/data/HCP_Raw/raw_data /data/HCP_Raw/derivatives/ participant \
--output-resolution 1.25 \
--output-space T1w \
--hmc-model eddy \
--fs-license-file /data2/Brian/random/license.txt \
--participant_label 105923 \
--work-dir /data/HCP_Raw/qsiprep/tmp_105923 \
--distortion-group-merge average \
--gpus all \
--eddy-config /data2/Brian/connectome_harmonics/eddy_config.json \
--skip-t1-based-spatial-normalization

I used --skip-t1-based-spatial-normalization in the hopes that this would leave everything in native T1w space. I don't have screenshots of the alignment with the default settings (i.e. using spatial normalization), but we had similar downstream issues, so I assume this misalignment issue remains. If you think this was the issue I can re-run with that setting off.

Do you know why we see this misalignment between the qsiprep preprocessed T1 and the native freesurfer segmentation? Is there a way we can configure qsiprep to output a T1 (and thus a T1 mask and 5tt) that are in the same space as the HCP T1w_acpc_dc_restore.nii, e.g.?

Thank you very much! Brian

Hello,

I am running qsiprep (0.12.2) on single-shelled DWI data that has already been run through Freesurfer (via fmriprep). Thus, I chose the recon spec for mrtrix single-shell ss3t. I use Slurm to submit my jobs, each subject using the following code:

#!/bin/bash
#SBATCH -t 48:00:00                  # walltime = 2 days
#SBATCH -N 1                         #  one node
#SBATCH -n 10                         #  10 CPU (hyperthreaded) cores
#SBATCH --gres=gpu:2                 #  2 GPU
#SBATCH --constraint=high-capacity   #  high-capacity GPU

singularity run --nv --cleanenv -B /om4 -B /om /om2/user/smeisler/qsiprep_new.img     \
/om/project/PARC/BIDS/data /om/project/PARC/BIDS/derivatives/ participant --participant-label $1 \
--fs-license-file /om4/group/gablab/dti_proc/license.txt --hmc_model eddy \
 --work_dir /om/project/PARC/BIDS/derivatives/work \
--recon_spec mrtrix_singleshell_ss3t_noACT --unringing_method mrdegibbs --output_resolution 1.2

Where $1 is the subject label passed into the script.

QSIPrep runs fine, but QSIRecon begins to throw errors, particularly during the "plot_peaks" task which begins concurrently with tractography. Since I run these jobs in the background with sbatch, I would expect something that requires a rendered window, like plot_peaks, to fail. The last successfully outputted file appears to be the normalized FODs in the /qsirecon/$SUB/dwi folder. The error is below.

	 [Node] Setting-up "qsirecon_wf.sub-ABCD1727_mrtrix_singleshell_ss3t_noACT.recon_wf.ss3t_csd.plot_peaks" in "/om/project/PARC/BIDS/derivatives/work/qsirecon_wf/sub-ABCD1727_mrtrix_singleshell_ss3t_noACT/recon_wf/ss3t_csd/_dwi_file_..om..project..PARC..BIDS..derivatives..qsiprep..sub-ABCD1727..dwi..sub-ABCD1727_space-T1w_desc-preproc_dwi.nii.gz/plot_peaks".
201113-13:30:42,349 nipype.workflow INFO:
	 [Node] Running "plot_peaks" ("qsiprep.interfaces.reports.ReconPeaksReport")
201113-13:31:48,948 nipype.workflow INFO:
	 b''
201113-13:31:48,948 nipype.workflow INFO:
	 b''
ERROR: In /work/standalone-x64-build/VTK-source/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 291
vtkXOpenGLRenderWindow (0x55b472eeae80): Could not find a decent config


ERROR: In /work/standalone-x64-build/VTK-source/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 291
vtkXOpenGLRenderWindow (0x55b472eeae80): Could not find a decent config


ERROR: In /work/standalone-x64-build/VTK-source/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 291
vtkXOpenGLRenderWindow (0x55b472eeae80): Could not find a decent config


ERROR: In /work/standalone-x64-build/VTK-source/Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 606
vtkXOpenGLRenderWindow (0x55b472eeae80): Cannot create GLX context.  Aborting.

Fatal Python error: Aborted

Current thread 0x00002b334da455c0 (most recent call first):
  File "/usr/local/miniconda/lib/python3.7/site-packages/fury/window.py", line 827 in record
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/niworkflows/viz/utils.py", line 847 in plot_peak_slice
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/niworkflows/viz/utils.py", line 867 in peak_slice_series
  File "/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/reports.py", line 745 in _run_interface
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741 in _run_command
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635 in _run_interface
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67 in run_node
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 232 in _process_worker
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99 in run
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297 in _bootstrap
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/spawn.py", line 118 in _main
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 297 in _serve_one
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 261 in main
  File "<string>", line 1 in <module>
exception calling callback for <Future at 0x2ba18e21d9b0 state=finished raised BrokenProcessPool>
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 324, in _invoke_callbacks
    callback(self)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
    result = args.result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
exception calling callback for <Future at 0x2ba18e21d710 state=finished raised BrokenProcessPool>
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 324, in _invoke_callbacks
    callback(self)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
    result = args.result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 324, in _invoke_callbacks
    callback(self)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
    result = args.result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

However, the slurm jobs have not cancelled yet. My question is does a failure in plot_peaks preclude the rest of the code from finishing? If so, should I be submitting jobs in another way that would allow for window rendering? I plan on waiting to see what happens regardless, but knowing the nature of tractography, I could be waiting for quite a bit.

Thanks, Steven

Hi, I'm currently exploring qsiprep v0.6.4 on Ubuntu 18.04 and encountered a problem with CUDA. Specifically, very early on, the pipeline throws the error

191120-19:50:44,55 nipype.workflow WARNING:
	 [Node] Error on "qsiprep_wf.single_subject_00012_wf.dwi_preproc_acq_NDDFC_run_01_wf.hmc_sdc_wf.eddy" (/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/eddy)
191120-19:50:45,885 nipype.workflow ERROR:
	 Node eddy failed to run on host Ixion.
191120-19:50:45,886 nipype.workflow ERROR:
	 Saving crash info to /work/wdir/bids50/derivatives/qsiprep/sub-00012/log/20191120-194715_25077cc2-befc-4960-8775-7c4f7057509b/crash-20191120-195045-eckhard-eddy-67060859-878b-4c86-8521-bf03601ca462.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/epi.py", line 766, in _run_interface
    runtime = super(Eddy, self)._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
eddy_cuda  --cnr_maps --flm=linear --ff=10.0 --acqp=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.bval --bvecs=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.bvec --imain=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.nii.gz --index=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/distorted_enhance/fill_holes/vol0000_TruncateImageIntensity_RescaleImage_mask_FillHoles.nii.gz --interp=spline --resamp=jac --niter=5 --nvoxhp=1000 --out=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --slm=linear
Standard output:

...................Allocated GPU # -1503168656...................
CUDA error after call to EddyGpuUtils::InitGpu
Error message: CUDA driver version is insufficient for CUDA runtime version
Standard error:

Return code: 1

In order to get this far, I had to manually link libcudart.so.7.5 by setting export SINGULARITYENV_LD_LIBRARY_PATH=/libs and specifying -B /usr/local/cuda-7.5/lib64:/libs in the call to singularity. Without it wouldn't find the CUDA runtime library and crash.

On the host I have CUDA 9.1 and NVIDIA driver version 390.132. Running the offending command (with eddy_cuda replaced by eddy_cuda9.1)

eddy_cuda9.1  --cnr_maps --flm=linear --ff=10.0 --acqp=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.bval --bvecs=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.bvec --imain=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/dwi_merge/vol0000_tcat.nii.gz --index=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/distorted_enhance/fill_holes/vol0000_TruncateImageIntensity_RescaleImage_mask_FillHoles.nii.gz --interp=spline --resamp=jac --niter=5 --nvoxhp=1000 --out=/work/qsiprep_wf/single_subject_00012_wf/dwi_preproc_acq_NDDFC_run_01_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --slm=linear

works well.

Does the singularity container have a CUDA 7.5 dependency built-in? And how does this square with the observation that eddy_cuda seems to support only version 8.0 and 9.1?

Thanks for tying to help figure this out!

I am trying to run qsiprep and running into issues. I've attached a screenshot of the error I'm getting. I'm not sure why its occurring. It says "Sentry is attempting to send 2 pending error messages" but I'm not sure what that means or how to receive the error messages. The error always occurs after "Finished "ds_interactive_report" " and occurs whether I use a T1w or --dwi-only flag turned on.

I have inspected the outputted html file and it says that there are no errors to report.

The command that I use is the following:

docker run -ti --rm \
    -v ~/Desktop/test/myProj:/data \
    -v ~/Desktop/test/out:/out \
    -v ~/Desktop/test/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    /data /out participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --output-resolution 1.2 \
        --verbose

I have also included an example of the filesystem tree I'm using. It passes the BIDS checker, but I'm wondering if there is something the checker is missing that is causing issues.

I processed the dsi dataset acquired with AP and PA direction, the data format is Philips enhanced dicom. I used dcm2niix to convert them into BIDS dataset and manually modified j and j- in phaseencodingdirection option in json files. #I do not acquired T1w data, so I used --dwi-only option. My code is shown below:

qsiprep-docker $bids_root_dir $bids_root_dir/out
participant
--participant-label $subj
--skip-bids-validation
--verbose
--stop-on-first-crash
--dwi-only
--b0-threshold 100
--denoise-method dwidenoise
--unringing-method mrdegibbs
--distortion-group-merge average
--hmc-model 3dSHORE
--write_graph
--fs-license-file /Users/chenli/freesurfer/license.txt
--nthreads $nthreads
--output_resolution 2.5

However I got the error message as below:

///Node: qsiprep_wf.single_subject_1_wf.sub_1_run_1_final_merge_wf.dwi_derivatives_wf.ds_optimization Working directory: /tmp/work/qsiprep_wf/single_subject_1_wf/sub_1_run_1_final_merge_wf/dwi_derivatives_wf/ds_optimization

Node inputs:

base_directory = /out compress = desc = extension = extra_values = in_file = keep_dtype = False source_file = dwi/sub-1_run-1_dwi.nii.gz space = suffix = hmcOptimization

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command result = self._interface.run(cwd=outdir, ignore_exception=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 388, in run self._check_mandatory_inputs() File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs raise ValueError(msg) ValueError: DerivativesDataSink requires a value for input 'in_file'. For a list of required inputs, see DerivativesDataSink.help()

When creating this crashfile, the results file corresponding to the node could not be found.///

I am confused about DerivativesDataSink node. Is it due to lack of anatomical images? Anyone can give some suggestions about this?

Hi! I'm getting this error when running qsiprep 0.16.1 on my data. The two DWI sequences have 45 volumes each, one is AP and the other PA direction. There are no specific fmaps, and there are 2 T1ws being averaged. I was hoping to use TOPUP/PEPOLAR for SDC, so I'm wondering if there isn't anything weird in the DWI JSONs that'd be causing issues when combining the data down the road?

Here's my call to qsiprep:

qsiprep ${TMPDIR}/BIDS/ ${tmp_out_dir} participant \
    --participant_label sub-${s} -w ${wrk_dir} \
    --notrack --nthreads $SLURM_CPUS_PER_TASK \
    --mem_mb $(( SLURM_MEM_PER_NODE - 2048 )) \
    --stop-on-first-crash \
    --unringing-method mrdegibbs \
    --output-resolution 1.2 \
    --template MNI152NLin2009cAsym \
    --distortion-group-merge average \
    --fs-license-file /usr/local/apps/freesurfer/license.txt

Here's how one of the DWI jsons look like: (the other one is similar, but PhaseEncodingDirection: j-)

(dcm2niix) [[email protected] sub-test4]$ cat ses-baseline/dwi/sub-test4_ses-baseline_dir-AP_run-1_dwi.json 
{
  "Modality": "MR",
  "MagneticFieldStrength": 3,
  "ImagingFrequency": 127.824,
  "Manufacturer": "GE",
  "InternalPulseSequenceName": "EPI2",
  "ManufacturersModelName": "DISCOVERY MR750",
  "InstitutionName": "NIH FMRIF",
  "DeviceSerialNumber": "000301496MR3T5MR",
  "StationName": "fmrif3ta",
  "BodyPartExamined": "HEAD",
  "PatientPosition": "HFS",
  "ProcedureStepDescription": "MRI Brain",
  "SoftwareVersions": "27\\LX\\MR Software release:DV26.0_R03_1831.b",
  "MRAcquisitionType": "2D",
  "SeriesDescription": "EDTI_2mm_MB2_cdif45_AP",
  "ProtocolName": "[XT-ID:20-HG-0147]_NCR_3",
  "ScanningSequence": "EP\\RM",
  "SequenceVariant": "NONE",
  "ScanOptions": "CL_GEMS\\SAT_GEMS\\EDR_GEMS\\EPI_GEMS\\HYPERBAND_GEMS\\PFF\\FS",
  "PulseSequenceName": "edti",
  "ImageType": [
    "ORIGINAL",
    "PRIMARY",
    "OTHER"
  ],
  "SeriesNumber": 14,
  "AcquisitionTime": "14:50:55.000000",
  "AcquisitionNumber": 1,
  "SliceThickness": 2,
  "SpacingBetweenSlices": 2,
  "SAR": 0.410538,
  "EchoTime": 0.088,
  "RepetitionTime": 5.826,
  "FlipAngle": 90,
  "PhaseEncodingPolarityGE": "Flipped",
  "ShimSetting": [
    3,
    3,
    -17
  ],
  "PrescanReuseString": "RN/s7",
  "CoilString": "32Ch Head",
  "MultibandAccelerationFactor": 2,
  "PercentPhaseFOV": 100,
  "PercentSampling": 100,
  "AcquisitionMatrixPE": 110,
  "ReconMatrixPE": 128,
  "EffectiveEchoSpacing": 0.000601323,
  "TotalReadoutTime": 0.076368,
  "PixelBandwidth": 3906.25,
  "PhaseEncodingDirection": "j",
  "ImageOrientationPatientDICOM": [
    1,
    -0,
    0,
    -0,
    1,
    0
  ],
  "InPlanePhaseEncodingDirectionDICOM": "COL",
  "ConversionSoftware": "dcm2niix",
  "ConversionSoftwareVersion": "v1.0.20220720",
  "MultipartID": "dwi_1"
}

(I added MultipartID manually to see if it'd help the issue, but it didn't).

The crash log is attached crash-20221223-182440-sudregp-concat-e65edb77-6e5c-4b05-9e24-ecb7ac025533.txt. And for completeness, here's the initial qsiprep output:

This dataset appears to be BIDS compatible.
        Summary:                  Available Tasks:        Available Modalities: 
        18 Files, 197.13MB                                T1w                   
        1 - Subject                                       dwi                   
        1 - Session                                       bold                  


        If you have any questions, please post on https://neurostars.org/tags/bids.

221223-16:28:01,860 nipype.workflow INFO:         Running with omp_nthreads=8, nthreads=32
221223-16:28:01,860 nipype.workflow IMPORTANT:
         
    Running qsiprep version 0.16.1:
      * BIDS dataset path: /lscratch/54848062/31942/BIDS.
      * Participant list: ['test4'].
      * Run identifier: 20221223-162801_14cbc70e-5f4a-4537-80a6-cd3e18659b17.
    
221223-16:28:02,847 nipype.workflow INFO:         Combining all dwi files within each available session:
221223-16:28:02,847 nipype.workflow INFO:
                - 2 scans in session baseline
221223-16:28:02,861 nipype.workflow INFO:
         [{'dwi_series': ['/lscratch/54848062/31942/BIDS/sub-test4/ses-baseline/dwi/sub-test4_ses-baseline_dir-AP_run-1_dwi.nii.gz'], 'dwi_ser
ies_pedir': 'j', 'fieldmap_info': {'suffix': 'rpe_series', 'rpe_series': ['/lscratch/54848062/31942/BIDS/sub-test4/ses-baseline/dwi/sub-test4_
ses-baseline_dir-PA_run-1_dwi.nii.gz']}, 'concatenated_bids_name': 'sub-test4_ses-baseline_run-1'}]221223-16:28:02,924 nipype.workflow IMPORTANT:
         Creating dwi processing workflow "dwi_preproc_ses_baseline_run_1_wf" to produce output sub-test4_ses-baseline_run-1 (1.05 GB / 55 DWI
s). Memory resampled/largemem=1.21/1.26 GB.

Let me know if you need more details!

Thanks,

Gustavo

Hi, I was running subjects with DSI data through the DWI pipeline, it had outputted HMC optimization for around 4 subject before crashing, I ran it twice from the start and it happened both times (thinking due to CPU usage),

I want to rerun from the crash regulating the CPU and to not have to preprocess everything again, the derivatives folder is still in place, but when I try to rerun it just hangs on the code below (tried to run with 1 participant and left it for a few hours it didn't budge)

This is the code I was rerunning with,

qsiprep-docker
$input $output participant
--output-resolution 1
--fs-license-file $fs_license
-w $intermediate_results
--stop-on-first-crash
--dwi-only
--hmc-model 3dSHORE
--nthreads 3

any ideas ?

The DSI Studio ATK reconstruction workflow can't limit cpu usage.

TODO:

• [ ] Try to figure out how to run this in a shared HPC environment without getting killed
• [ ] Add whatever strategy works to documentation