Open chiuhoward opened 1 week ago
Updates: I tried two other things and they both didn't work:
--anatomical-template MNIInfant
argument. This returned qsiprep: error: argument --anatomical-template: invalid choice: 'MNIInfant' (choose from 'MNI152NLin2009cAsym'
@tsalo This must have been a side effect of the templateflow PR. Also a good point that we don't have any infant tests.
@chiuhoward I'm not sure your binding strategy will work anymore because we're using templateflow instead of the built-in templates.
Were there issues with 0.21.4 when you used it? I think all the changes since 0.21.4 have been related to infrastructure and no new software/methods have changed
@mattcieslak The binding strategy worked with 0.21.4 - I never figured out the way to pass alternative templates into qsiprep “properly” so that was the bodge that worked for me.
How about the quality of the results? I don't think the actual processing will be that different, but you'll have a much more difficult time getting the alternative templates into later versions
@mattcieslak Yeah I think the quality wasn't great (with or without a reverse phase-encoding direction), hence I wanted to rerun with v23 since you mentioned that there have been many enhancements since then.
I am not committed to using specific alternative templates - using different templates was also just part of trying to optimize the dataset I had as the MNI Infant template seemed slightly larger than the neonatal ones, and I also tried varying other parameters like tractography method, cleaning, step size, angles, etc. There were too many possibilities, that's why I also wrote to ask what was "recommended" with 23.0.
Thank you both so much for looking into this @tsalo!
Summary
Tried to run qsiprep with the infant flag but the workflow was still expecting an adult template.
Additional details
What were you trying to do?
I am trying to preprocess the same data with the new version of qsiprep; I'd previously preprocessed the same dataset with qsiprep 0.21.4.
What did you expect to happen?
I expect the pipeline to run like it did previously (version 0.21.4).
What actually happened?
I looked in the documentation and the only option for
--anatomical-template
was MNI152NLin2009cAsym. I also noticed that in this version of the code, the templates were no longer bundled in theqsiprep/data
folder, so maybe I'd need a new way to pass templates into qsiprep?Reproducing the bug
I'd tried running the same script just by changing the singularity container to point back to 0.21.4 and it still initiates the pipeline.