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Dear Tibor,
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<div class="">Thanks for sharing.</div>
<div class="">Indeed coordinate systems (<a href="https://www.fieldtriptoolbox.org/faq/coordsys/#details-of-the-freesurfer-coordinate-system" class="">https://www.fieldtriptoolbox.org/faq/coordsys/#details-of-the-freesurfer-coordinate-system</a>) are a pain
in the bum. And indeed Freesurfer is notorious for having the surfaces expressed in a different coordinate system than the corresponding volumetric anatomicals. Specifically, where you mention ’typically’ a volume from the same FreeSurfer processing, I’d say
it is mandatory to use a reference image (e.g. T1.mgz or so, at least a volume that is in the /mri/ folder of a recon-all output) from the same FreeSurfer pipeline. Alternatively, one can run <a href="https://github.com/fieldtrip/fieldtrip/blob/master/bin/ft_postfreesurferscript.sh" class="">https://github.com/fieldtrip/fieldtrip/blob/master/bin/ft_postfreesurferscript.sh</a> on
the files in the /surf/ directory, which expresses the output surfaces in the same coordinate system as the input MRI images. (as per line 85 in the referenced shell script).</div>
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<div class="">Best wishes and keep up the good work,</div>
<div class=""><br class="">
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<div class="">JM<br class="">
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<blockquote type="cite" class="">
<div class="">On 20 Oct 2021, at 13:14, Tibor Auer via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Dear FieldTrippers,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I came across an issue when atlasing the source-level measures and the sourcemodel was estimated using FreeSurfer cortical sheet.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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The typical code to read the corresponding FreeSurfer annotation uses<span class="Apple-converted-space"> </span><i class="">ft_read_atlas</i>:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<i class=""> atlaslh = ft_read_atlas({‘label/lh.aparc.DKTatlas’,’surf/lh.pial’ },'format','freesurfer_aparc');<o:p class=""></o:p></i></div>
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<i class=""> atlasrh = ft_read_atlas({‘label/rh.aparc.DKTatlas’,’surf/rh.pial’ },'format','freesurfer_aparc');<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas = rmfield(atlaslh,'rgba');<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas.pos = vertcat(atlaslh.pos, atlasrh.pos);<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas.tri = vertcat(atlaslh.tri, atlasrh.tri+size(atlaslh.pos,1));<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas.aparclabel = vertcat(spm_file(atlaslh.aparclabel,'prefix','lh_'),spm_file(atlaslh.aparclabel,'prefix','rh_'));<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas.aparc = vertcat(atlaslh.aparc, atlasrh.aparc+numel(atlaslh.aparclabel));<o:p class=""></o:p></i></div>
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<o:p class=""> </o:p></div>
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The issue, however, is that the positions do not correspond to those of the sourcemodel. It is not a FieldTrip issue, but a more generic one. E.g. FSL:<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;19c45d5b.1803__;!!HJOPV4FYYWzcc1jazlU!s-pXYehuu6woMknmRYORhLOPZ2KHyp8vbG1ReYL_ocY5Ur7pbnHMxCIE2jCayGkh0Wu1LS1L-tAJ9Wc$" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">JISCMail
- FSL Archives</a>. FSL solves the issue by asking for a reference image (typically a volume from the same FreeSurfer processing). Based on the FSL codes for<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/apidoc/_modules/fsleyes/displaycontext/meshopts.html__;!!HJOPV4FYYWzcc1jazlU!s-pXYehuu6woMknmRYORhLOPZ2KHyp8vbG1ReYL_ocY5Ur7pbnHMxCIE2jCayGkh0Wu1LS1L6P1iGA4$" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">fsleyes</a><span class="Apple-converted-space"> </span>and<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://git.fmrib.ox.ac.uk/fsl/fslpy/-/blob/master/fsl/data/mghimage.py__;!!HJOPV4FYYWzcc1jazlU!s-pXYehuu6woMknmRYORhLOPZ2KHyp8vbG1ReYL_ocY5Ur7pbnHMxCIE2jCayGkh0Wu1LS1La76onHQ$" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">fsl.data.mghimage</a>,
I managed to implement something similar in MATLAB:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<i class=""> fsmri = MRIread(‘mri/T1.mgz’);<o:p class=""></o:p></i></div>
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<i class=""> sourceatlas = ft_transform_geometry(fsmri.vox2ras/fsmri.tkrvox2ras, sourceatlas);<o:p class=""></o:p></i></div>
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<o:p class=""> </o:p></div>
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After transformation, the sourceatlas will be aligned to the sourcemodel.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Kind regards,<o:p class=""></o:p></div>
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<span class="">Tibor<span class="Apple-converted-space"> </span></span><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<span class=""> </span><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(34, 42, 53);" class="">Auer, Tibor M.D. Ph.D.</span></b><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(0, 102, 255);" class="">Research Fellow</span></b><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="color: rgb(0, 102, 255);" class="">School of Psychology, Faculty of Health and Medical Sciences</span></b><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<span class="">University of Surrey, Guildford GU2 7XH</span><span lang="HU" class=""><o:p class=""></o:p></span></div>
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<span class=""><a href="mailto:T.Auer@surrey.ac.uk" style="color: rgb(5, 99, 193); text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">T.Auer@surrey.ac.uk</span></a></span><span lang="HU" class=""><o:p class=""></o:p></span></div>
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