Hi Leon

we can give you a version of mris_make_face_parcellation if you tell us what hardware/software environment you are running in, but it doesn not transfer annotations from one subject to another. For that you should use mri_surf2surf (I thought mri_label2label did this also, but I guess not).

cheers
Bruce


On Wed, 30 May 2012, Leon wrote:

> 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
> >>
> >> 1. 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?
> >>
> >> 2. 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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> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
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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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