Hello Hanne,
I’ll take a look with you and hopefully we can figure this out. Just to clarify, the mris_divide_parcellation outputs lh.aparc.splittedinsula.annot, but this is saved as a text file like lh.aparc.splittedinsula.txt?
Thanks so much! Matt
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Wednesday, December 30, 2020 at 10:29 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Anterior insula thickness {Disarmed}
External Email - Use Caution Dear experts,
I am trying to divide the insula into two parts, in order to calculate the thickness of only the anterior region. I used the command mris_divide_parcellation on the aparc.annot file (see below), with a text file that indicated which region needs to be split (splittable.txt). The issue is that it does generate a file, but as a document and not an annotation file. Supposedly the issue is with the seed (see last output line error). When trying to use this file regardless, to make the labels, it does not generate any labels (see second command and output).
Do you perhaps have a suggestion how I could fix this?
Best,
Hanne
Parcellation command: mris_divide_parcellation fsaverage lh lh.aparc.annot splittable.txt lh.aparc.splittedinsula.annot
Output: reading colortable from annotation file... colortable with 1036 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) interpreting 4th command line arg as split file name dividing insula (1035) into 2 parts allocating new colortable with 36 additional units... supposed to be reproducible but seed not set saving annotation to lh.aparc.splittedinsula.annot
Annot to label command: mri_annotation2label --subject fsaverage --hemi lh --annotation lh.aparc.splittedinsula.annot --outdir ..
Output: subject = fsaverage annotation = /Applications/freesurfer/FS/fsaverage/label/lh.aparc.splittedinsula.annot hemi = lh outdir = .. surface = white
Reading surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Loading annotations from /Applications/freesurfer/FS/fsaverage/label/lh.aparc.splittedinsula.annot reading colortable from annotation file... colortable with 1072 entries read (originally none) Seg base 0 max index = 1037 Segmentation fault: 11
On 23 Dec 2020, at 19:02, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:
We don't have an anterior insula segmentation. One thin you can try is to divide the insula label with mris_divide_parcellation. If one of those subdivisions works for you then you can compute the thickness inside it. You might want to do it on fsaverage and then map it back to the individual subjects. Or you can just draw the label you want on fsaverage and map it back to the individual subjects On 12/21/2020 9:34 AM, Hanne Van Der Heijden wrote: External Email - Use Caution Dear freesurfer experts,
I have a question regarding analysis of cortical thickness. In the stats folder of each subject, the {hemi}.aparc.stats file gives the thickness of several areas, one of them being the insula. Is it possible to get only the anterior insula thickness?
Thank you in advance, and I hope to hear from you soon.
Best,
Hanne van der Heijden
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