PhaseEncodingDirection_QSiprep Help

[eUgwueke]

Hello Team,
I am new to qsiprep and I have encountered this problem severally.
I have pepolar images AP direction as j- and dwi images as j for the phase encoding direction. When I run qsiprep, the outputs shows the summary with the correct input direction in the json file but in the Diffusion summary, it shows it as Anterior to Posterior. I have tried to reverse the directions yet it still gives the same output as AP instead of PA.

I am using verison 19 of qsiprep.

Command used :

apptainer run --containall --writable-tmpfs \
    -B $qsiprepPath:$qsiprepPath \
    -B $outPath:$outPath \
    -B $cachePath:$cachePath \
    -B $licFile:/opt/freesurfer/license.txt \
    qsiprep-0.19.0.sif \
    $qsiprepPath $outPath participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --skip-bids-validation \
    --pepolar-method TOPUP \
    --hmc_transform Affine \
    --hmc_model eddy \
    --longitudinal \
    --skull_strip_template OASIS \
    --anatomical-template MNI152NLin2009cAsym \
    --anat-modality T1w \
    --output-resolution 1.2 \
    --participant-label $participant_label \
    --nthreads 5 \
    --low-mem \
    --stop-on-first-crash \
    -w $cachePath

my data is arranged

the results i complained about

[Steven]

Hi @eUgwueke,

Can you try updating qsiprep and trying again? I would not change anything within the JSONS, assuming conversion from dicoms to bids is correct. In any case, this might just be an error in the htmls, but the data itself could be fine. It might also be the case that the report is saying that it is some direction along anterior-to-posterior (that is, it is either j or j-, but not any i or k variant).

Best,
Steven

[eUgwueke]

I will update qsiprep and see if anything changes. Thank you.

[eUgwueke]

Hello @Steven,

1. I successfully used qsiprep version 22.0, and the results remained the same. I guess it’s the results just as you mentioned to be in that direction.

2. I was faced with a challenge while running the same code but with qsiprep-1.0.0rc1.sif, its shows this error

**........................**
**dti60b1000_dwi_LAS_denoised.nii.gz"e[0K**
**	e[?7l**
**	dwidenoise: [ 13%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 25%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 38%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 50%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 63%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 75%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7he[?7l**
**	dwidenoise: [ 88%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"...e[0Ke[?7h**
**	dwidenoise: [100%] compressing image "sub-NCANDA00033_ses-Y01_acq-dti60b1000_dwi_LAS_noise.nii.gz"e[0K**
**Traceback:**
**	Traceback (most recent call last):**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 402, in run**
**	    runtime = self._post_run_hook(runtime)**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/mixins/reporting.py", line 49, in _post_run_hook**
**	    self._generate_report()**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/denoise.py", line 107, in _generate_report**
**	    compose_view(**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/niworkflows/viz/utils.py", line 401, in compose_view**
**	    out_file.write_text("\n".join(_compose_view(bg_svgs, fg_svgs, ref=ref)))**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/niworkflows/viz/utils.py", line 459, in _compose_view**
**	    fig.save(str(out_file))**
**	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/svgutils/transform.py", line 321, in save**
**	    fid.write(out)**
**	OSError: [Errno 28] No space left on device**

It shows that the run starts to generate outputs but suddenly it’s interrupted with the memory issue. Never experienced that with other versions.What could cause this?

[Steven]

Hi @eUgwueke,

For the second error, what happens if you remove the --containall flag and instead just use -e?

Best,
Steven

[eUgwueke]

It worked fine. Thanks.

However, the outputs doesn’t include a DWI sampling scheme for this version. Is that it?