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
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
____________________________________________________________________________
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
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
