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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">Dear FieldTrip list<span></span></p>

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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">Has anyone here imported individual atlases from Freesurfer into FieldTrip? It should be possible with ft_read_atlas. From the documentation of ft_read_atlas: <span></span></p>

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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif"><i>  For individual surface-based atlases from FreeSurfer, you should specify two <span></span></i></p>

<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif"><i>  filenames as a cell-array: the first points to the file that contains information<span></span></i></p>

<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif"><i>  with respect to the parcels' labels, the second points to the file that defines the<span></span></i></p>

<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif"><i>  mesh on which the parcellation is defined.<span></span></i></p>

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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">Ft_read_atlas require a struct containing the filename of the atlas file and the cortical surface/mesh. However, I keep getting errors that ft_read_atlas cannot read Freesurfers “annot” files: “ <i>unrecognized filetype 'freesurfer_annot'.</i>“ I get a similar error when I try to read Freesurfer “label” files.<span></span></p>

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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">The problem seems to be because ft_read_atlas calls ft_read_mri which does not support the type 'freesurfer_annot'. My question is how to read in Freesurfer annotations or labels? Do I need to convert the Freesurfer files first or is there another step I need to do first? If anyone has managed to read Freesurfer labels in FieldTrip, I will be delighted to hear the answer.<span></span></p>

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<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">Best regards<span></span></p>

<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif">Mikkel</p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:"Calibri",sans-serif"><br><span></span></p>





<div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><font size="1"><span style="font-family:arial,helvetica,sans-serif">Mikkel C. Vinding<br>NatMEG, Karolinska Institutet<b><br>
</b>Nobels väg 9<br>171 77 Stockholm, Sweden<b><br>
</b>Email: <a href="mailto:mikkel.vinding@ki.se" target="_blank">mikkel.vinding@ki.se</a><b><br>
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