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bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
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Adding the -notal-check flag #84

Open augustoielo opened 6 months ago

augustoielo commented 6 months ago

Hi, I need to skip the automatic failure detection of Talairach alignment for a few subject (-notal-check flag). Perhaps I missed something in the documentation, but I couldn't find a way to do it. Is there a way to add flags to the execution? Thanks.

Remi-Gau commented 6 months ago

from a quick check in the argument parser this is not an argument passed to the freesurfer

https://github.com/bids-apps/freesurfer/blob/master/run.py#L44

Can you point to the doc page in freesurfer related to this flag?

augustoielo commented 6 months ago

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview

FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix in a file called talairach.xfm and is located in the /mri/transforms directory. Under some circumstances, the alignment can fail the automatic failure detection scheme (-tal-check flag, which can be disabled via -notal-check).