if you use ?h.sphere it will generate a parcellation this is uniform in
subject space, if you use sphere.reg it will generate one that is uniform
in fsaverage space (and in which the parcels can be compared across
subjects). They are *not* anatomical though, in the sense that the aparcs
correspond to gyri and sulci
cheers
Bruce
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 ([email protected]) (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 <[email protected]>
To: Leon <[email protected]>
Cc: FreeSurfer <[email protected]>
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/[email protected]/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
> >> [email protected]
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
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> >
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> > addressed. If you believe this e-mail was sent to you in error and the
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> ____________________________________________________________________________
> From: Bruce Fischl <[email protected]>
> To: Leon <[email protected]>
> Cc: FreeSurfer <[email protected]>
> 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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>
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