Mathias Goncalves

@juansanchezpena just to avoid any confusion - the LTS is 20.2.x. FreeSurfer 7 was included 22.0.x, the latest release being 22.0.1. If you want to hold off until later today...

will need to update circle's docker orb

https://github.com/nipreps/fmriprep/commit/4feb341048a01d74eb6c6ce77496f19f42d2a9bf

May be worth checking all of the `_alway_run` recon interfaces too. https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L225 https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L386 https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L406 https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L418 https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L432 https://github.com/nipreps/smriprep/blob/791d31328af33d8342627d0419f10dda25b8b842/smriprep/workflows/surfaces.py#L442

This was fixed in https://github.com/nipreps/smriprep/issues/416, hoping to get a new release out with the fix this week. BTW, I believe the `MNIPediatricAsym:res-2:cohort-5` in your command should be `MNIPediatricAsym:cohort-5:res-2`, as cohort...

Please re-open if further discussion is needed

Hi @droediger, thanks for posting on this - we hoped #2879 would address this, but it seems there are still cases (potentially due to imperfect segmentations?) where these zeroes can...

Ah yes, the HCP snippet I linked was for subcortical processing. IIRC, we were hesitant to add dilation because it could potentially mask a problem in the implementation. Processing some...

I had just tested this within a docker container and the two files listed above were present. Probably because we are connecting them to `outputnodes` somewhere..

https://github.com/nipy/nipype/blob/ca27e5187e3c12be5b5565c73be40f7ae70c1689/nipype/interfaces/dcm2nii.py#L449-L450 IIRC, dcm2niix uses (used?) 1 return codes for warnings (but conversion still occurred), and 2+ for serious problems where conversion was not possible.