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Hi Pierpaolo,
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<div class="">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.</div>
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<div class="">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.</div>
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<div class="">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.</div>
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<div class="">Based on my reading of the code, either of the following 2 would work:</div>
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<div class="">atlas = ft_read_atlas({‘label/lh.<blabla>.annot’ ‘surf/lh.orig’}, ‘format’, 'freesurfer_aparc')</div>
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<div class="">atlas = ft_read_atlas(‘aparc.mgz’)</div>
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<div class="">combining information from a surface-based representation: lh.<etc> and volume-based represenation: <etc>.mgz for sure is not going to do the trick.</div>
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<div class="">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)!</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 1 Jun 2022, at 11:12, Pierpaolo Croce via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div dir="ltr" class="">Dear List,
<div class="">I'm trying to read the single subject atlas obtained from FreeSurfer segmentation, </div>
<div class="">The code i'm using is : </div>
<div class=""> 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')<br class="">
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<div class="">My problem is that I don't know which if the files that i pass are correct</div>
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<div dir="ltr" class="">Ing. Pierpaolo Croce, PhD.<br class="">
Institute for Advanced Biomedical Technologies - ITAB<br class="">
and<br class="">
Department of Neuroscience and Imaging<br class="">
University of Chieti "G. D'Annunzio"<br class="">
Via dei Vestini, 33<br class="">
66013 Chieti, Italy</div>
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