Adding the -notal-check flag

[augustoielo]

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]

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]

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).