Hi, Bruce
Thank you for the information. I went through the archive again and found this post (see below). It seems that this is exactly what I want to do. However, I tried mris_make_face_parcellation and found that with my 5.1 version, no matter what my input is (?h.sphere or ?h.sphere.reg), I always get identical results, same as Franz. Do you know how I can get the updated version of the function in which the bug has been fixed?
Also, I have the same question as Franz does: (1) which is a better way to transfer annotation file (here is ic?.tri), using mri_surf2surf or using mris_make_face_parcellation with the input surface of ?h.sphere.reg? (2) I tried mri_label2label and it seems it does not read annotation file. Could you let me know why I should use mri_label2label instead of mri_surf2surf with "-sval-annot" option?
Sorry for so many questions as I am new to FreeSurfer and your help is greatly appreciated!
Leon
Re: [Freesurfer] mris_make_face_parcellation
Franz Liem Mon, 13 Feb 2012 05:35:10 -0800
Dear Bruce,
thank you so much for your reply; it seems to work now.
However, a weird thing, I also mentioned in my previous post, still happens: when using ic3 there are duplicate labels in the newly created annotations.
at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (in fsaverage lh: cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (in fsaverage lh: cluster 1 around vertex 137845, cluster 2 around vertex 155417)
Is there a way to avoid this?
Thanks for your help, Franz
Am 26.01.2012 um 14:47 schrieb Bruce Fischl:
Hi Franz
looks like this was a bug in mris_make_face_parcellation, which I just fixed. It was always using the sphere regardless of what you specified. Krish: can you get Franz a new mac version of it to try out?
sorry Bruce
On Thu, 26 Jan 2012, Franz Liem wrote:
Dear Freesurfers,
I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0).
I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot
- It seems not to make a difference whether I choose .sphere or
.sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially). According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html): "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects"
Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it?
Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )?
To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually?
- There seems to be duplicate structNames/annotationValues when applying
mris_make_face_parcellation with ic3.tri In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come?
Thanks for you help, Franz
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________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 30, 2012 3:02 PM Subject: Re: [Freesurfer] transfer annot files from template to each subject
Hi Leon
I think mri_label2label should do the trick
cheers Bruce On Wed, 30 May 2012, Leon wrote:
Hi, FreeSurfer expert I am having difficulty finding the functions that transfer an annotation file I generated on a template to each subject. This template has been registered with several subjects using a surface-based registration method. Now what I want is to (1) transfer this annotation file from the template to each subject, through surface-based registration. and then (2) transfer the annotation file in each subject's surface to their T1 volume space.
Could someone show me which functions I need to use? Do I have to convert the annotation files first to label files to do that?
Many thanks in advance
Leon
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