Hi, Bruce
Thank you very much for your information and the codes.
Best
Leon
________________________________
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: Leon <leonad...@yahoo.com>
Sent: Friday, June 1, 2012 10:48 AM
Subject: Re: [Freesurfer] transfer annot files from template to each subject
p.s. here's a gzipped version of mris_make_face_parcellation you can try
out
On Thu, 31 May 2012, Leon wrote:
> Hi, Bruce
>
> Here is the information of my linux:
>
> Linux version 2.6.18-308.4.1.el5 (mockbu...@hs20-bc2-4.build.redhat.com) (gcc
> version 4.1.2 20080704
> (Red Hat 4.1.2-52)) #1 SMP Wed Mar 28 01:54:56 EDT 2012
> I think that I have figured out how to realize that by checking the archives.
> I first used
> mri_surf2surf to transfer ROIs from the template surface to subjects'
> surfaces, and then used
> mri_label2vol to transfer the ROIs from each subject's surface to its volume.
> Correct me if I am not
> heading toward the right direction.
>
> Going back to llc_make_face_parcellation, if it cannot be used to transfer
> ROIs between subjects, what
> is the difference between providing ?h.sphere and ?h.sphere.reg as the input
> surface?
>
> Thanks again for your help!
> Leon
>
> _______________________________________________________________________________________________________
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> To: Leon <leonad...@yahoo.com>
> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
> Sent: Thursday, May 31, 2012 2:37 PM
> Subject: Re: [Freesurfer] transfer annot files from template to each subject
>
> 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
> > >>
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >>
> > >>
> > >>
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> >
> > ____________________________________________________________________________
> > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> > To: Leon <leonad...@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
> > >
> > >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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> > e-mail
> > contains patient information, please contact the Partners Compliance
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> >
> >
> >
> >
>
>
>
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