Hmm, found the problem. These two labels represent 'non-cortex' areas and are therefore zero. They where however wrongly mapped further in my script.
Conclusion: everything works as it should work. :-).
---------- Forwarded message ---------- From: Martijn Steenwijk martijnsteenwijk@gmail.com Date: Thu, Dec 22, 2011 at 1:53 PM Subject: Re: [Freesurfer] Reading annotation file in Matlab To: Thomas Yeo ythomas@csail.mit.edu Cc: freesurfer@nmr.mgh.harvard.edu
You are right. I found out the same using the wiki http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles. However, I discovered that read_annotation.m reads some labels as zeros and 'misses' labels 1639705 and 3294840 defined in the enclosed LUT while reading for example lh.aparc.annot resulting from a standard execution of the pipeline (recon-all -all).
Do you have any thoughts on this? Is this a bug (either in the stored .annot or during the reading process)?
Thanks for sharing your thoughts,
Best, Martijn
On Thu, Dec 22, 2011 at 1:20 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi, I am not sure if your question is about read_annotation or aparc.annot in particular.
read_annotation.m reads the labels embedded in the annotation file you passed to it. The labels embedded in the annotation file may or may not be the same as those in FreeSurferColorLUT.
I could be wrong, but in the case of aparc.annot generated by recon-all, I don't think the labels correspond to those in FreeSurferColorLUT.
--Thomas
On Thu, Dec 22, 2011 at 6:23 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:
Dear all,
I'm trying to read aparc.annot into Matlab using the matlab/read_annotation.m function. Is it correct that the labels read by this function do not correspond with for example the FreeSurferColorLUT?
Are the labels stored as 16 bit (unsigned)integers, or in another way?
Best, Martijn
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