How do I run the reorient_fslstd reconstruction after successful preprocessing?

1

I was hoping to convert my preprocessed qsiprep data to fslstd and thought the following would work

qsiprep-docker derivatives/qsiprep derivatives participant --recon_input derivatives/qsiprep --recon_spec reorient_fslstd --fs-license-file /home/weberam2/license.txt

But then it says I need to include --output-resolution, which seems weird.

If I add the same --output-resolution argument I used for preprocessing, I get the following error

Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 938, in build_qsiprep_workflow
    retval['workflow'] = init_qsiprep_wf(
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/base.py", line 229, in init_qsiprep_wf
    single_subject_wf = init_single_subject_wf(
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/base.py", line 491, in init_single_subject_wf
    raise Exception("No dwi images found for participant {}. "
Exception: No dwi images found for participant AMW01. All workflows require dwi images unless --anat-only is specified.
qsiprep: Please report errors to https://github.com/pennbbl/qsiprep/issues

I feel like I’m probably doing something wrong?

3

Disregard my last answer. I am guessing that the qsiprep-docker command does not automatically mount the --recon-input argument (which if true, should be raised as a bug in GitHub - PennLINC/qsiprep: Preprocessing and reconstruction of diffusion MRI, and now I wonder if the same is true for other paths such as freesurfer input). You may have to use the docker run version of qsiprep, instead of the nice wrapper function.

EDIT2: Disregard BOTH of the prior answers.

Your BIDS input argument is derivatives. Instead, it should still be the original bids dataset (that same path you pointed QSIPrep to when preprocessing, presumably).

Best,
Steven

4

Hi Steven,

I think you are correct. Thank you for your response(s)!
The reason I wrote it that way was because of how I interpreted the instructions. I wonder if they could be made more clear for people in the future? Unless I’m the only one who makes this mistake :smiley:

Cheers,

Alex W.