Roeland Hancock

I’ve seen something similar happen when the input T1 has been preprocessed with intensity normalization. Is this the case in your data, eg does the white matter have an intensity...

Indeed that doesn't look like a preprocessed image. The data does not look very good though—I would expect to see some grey matter near your cursor. Could be a quality...

Has any one tried this https://github.com/DCAN-Labs/abcd-hcp-pipeline? It looks there's a version of the HCP pipeline for ABCD. On Thu, Feb 24, 2022 at 9:58 AM Giulia Bertò ***@***.***> wrote: >...

It looks like the JSON sidecar associated with the T1w you are trying to process does not have a 'DwellTime' field. The DwellTime value is required for correcting distortion in...

@rhancockn Add error handling around `t1_spacing = layout.get_metadata(t1ws[0])["DwellTime"]` (and maybe `t2_spacing = layout.get_metadata(t2ws[0])["DwellTime"]`). If distortion correction is to be done, throw a descriptive error message about why this field is...

That's right; the default --processing-mode hcp will require a DwellTime for the T1w and T2w volumes. On Fri, Jan 22, 2021 at 9:10 AM Giulia Bertò wrote: > Thank you...

Does your dataset have phase/magnitude fieldmaps? That should work, but hasn’t been tested as thoroughly as the HCP style of collecting spin echo images with opposing PE direction. Would you...

This is very helpful-it looks like the code could better handle the presence of both epi and phase/magnitude fieldmaps. However, you do have incomplete data. EPI fieldmaps come in pairs...

I think making use of the existing `acq-` and `rec-` labels provided in the BIDS spec is the way to go, and seems to be the intended purpose of these...