-
Notifications
You must be signed in to change notification settings - Fork 38
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
23.2.0a3: template_iterator_wf.select_xfm
failing with MNIPediatricAsym
when cohort specified
#407
Comments
Interesting. Seems to be the cohort/res combo. Can you share |
|
I see. So the issue is that we currently pass around template as if it's meaningful on its own, because resolutions are not considered distinct templates (you can register to 1 and resample to 2). But cohorts should be considered distinct templates, so we need to pass around cohort information. Right now we pass smriprep/smriprep/workflows/fit/registration.py Lines 205 to 208 in 8830bf8
And this needs to be combined into smriprep/smriprep/workflows/anatomical.py Lines 971 to 1013 in 8830bf8
Another approach is to pass around One thing that seems clear to me is that we'll need to add That will require updates to the path patterns in niworkflows: https://github.com/nipreps/niworkflows/blob/a0af2636521580d84b6b4eb1c32b0cfc4e1bff85/niworkflows/data/nipreps.json#L154-L184 As well as adding the cohort to the how we look up precomputed transforms in: smriprep/smriprep/utils/bids.py Lines 53 to 63 in 8830bf8
Which is called here: smriprep/smriprep/workflows/base.py Lines 365 to 369 in 8830bf8
If any changes are needed to the last part, they'll need to be propagated to fMRIPrep here: |
I can give it a shot. I shouldn't have trouble setting up a dev environment (changes will be happening in https://github.com/smeisler/smriprep/tree/fix/cohort_res) but will update here if I run into issues. |
select_xfm
failing with MNIPediatricAsym
select_xfm
failing with MNIPediatricAsym
when resolution specified
Actually before I do too much, I should make sure the dev environment was set up correctly. Steps I took:
Anything I'm missing? I realize it's not containerized, so there might be some oddities with software versions I have on my computer, but hopefully I can at least make the changes to the workflow. |
You're going to need to work with niworkflows and you'll at least want to test with fmriprep, so I think you'll want to install all of these: for REPO in nipreps/{fmriprep,smriprep,niworkflows}; do
git clone https://github.com/$REPO
done
mamba env create -f fmriprep/env.yml # Can use -n to override the default name of fmriprep
mamba env config vars set -n fmriprep FSLDIR=$CONDA_PREFIX # Make sure FSL tools can find each other
mamba activate fmriprep
pip install --no-deps -e ./fmriprep -e ./smriprep -e ./niworkflows It's not hard to add additional repos after the fact. You'll also need FreeSurfer, AFNI and Connectome Workbench installed in your PATH, but otherwise you should be good to go. Edit: Note that I reordered one command. You want to set the environment variable before activating to make sure it gets loaded into your shell. |
select_xfm
failing with MNIPediatricAsym
when resolution specifiedselect_xfm
failing with MNIPediatricAsym
when cohort specified
select_xfm
failing with MNIPediatricAsym
when cohort specifiedtemplate_iterator_wf.select_xfm
failing with MNIPediatricAsym
when cohort specified
@smeisler Just checking in about how this is going for you. |
Haven't had much time to work on this yet, hope to get to it tomorrow. |
Hello @smeisler have you had any luck? I am facing the same issue but using MNIInfant:cohort-2. |
Hi @effigies I have the same issue: Best, |
If you use the :unstable tag, you can test the next version prior to release. |
Hi @effigies, I tested the current _: unstable _ version with _ MNIPediatricAsym: res-2:cohert-6 _. Everything worked fine for me and did not produce any errors, so I'm looking forward to the 22.2.3 release. Thanks for all the effort, Florian |
The release that will be included in will be 24.0.0. |
What happened?
select_xfm
is failing onWhat command did you use?
What version of fMRIPrep are you running?
23.2.0a3
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
No
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
BIDS Validator outputs below. I don't think any of these errors would be related to the present error.
The text was updated successfully, but these errors were encountered: