[FieldTrip] read freesurfer atlas

[Schoffelen, J.M. (Jan Mathijs)]

Hi Pierpaolo,

It is unclear what your aim is, i.e. what you want read in, so it is hard to guess for me what an optimal answer would be.

Indeed it does not make sense to try and combine all pairs of freesurfer generated output files to find out which combination automagically works, although in theory that is possible.

An alternative is to read a bit in the relevant parts of the ft_read_atlas code to try and figure out a bit more what’s going on.

Based on my reading of the code, either of the following 2 would work:

atlas = ft_read_atlas({‘label/lh.<blabla>.annot’ ‘surf/lh.orig’}, ‘format’, 'freesurfer_aparc')

atlas = ft_read_atlas(‘aparc.mgz’)

combining information from a surface-based representation: lh.<etc> and volume-based represenation: <etc>.mgz for sure is not going to do the trick.

If you feel that the documentation of the function can be improved: we look forward to your suggestions (of course ideally as a pull request into the fieldtrip repository)!

Best wishes,
Jan-Mathijs



On 1 Jun 2022, at 11:12, Pierpaolo Croce via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear List,
I'm trying to read the single subject atlas obtained from FreeSurfer segmentation,
The code i'm using is :
    atlas = ft_read_atlas({'\\wsl$\Ubuntu-18.04\usr\local\freesurfer\7-dev\subjects\MONK001\label\lh.aparc.annot', '\\wsl$\Ubuntu-18.04\usr\local\freesurfer\7-dev\subjects\MONK001\mri\aseg.mgz'}, 'format' ,  'freesurfer_aparc')

My problem is that I don't know which if the files that i pass are correct
--

Ing. Pierpaolo Croce, PhD.
Institute for Advanced Biomedical Technologies - ITAB
and
Department of Neuroscience and Imaging
University of Chieti "G. D'Annunzio"
Via dei Vestini, 33
66013 Chieti, Italy
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