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Hi Doug
THIS WORKED!!! Thank you so much for all your help!
Trisanna
--
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Monday, November 8, 2021 1:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2label issues
Try this: register the old/1st recon to the second with
bbregister --mov old/mri/nu.mgz --targ newsubject --t1 --reg reg.lta
Map the old surface into the new space
mris_apply_reg --lta reg.lta old/surf/lh.white newsubject/surf/lh.white.old
Verify that the old surface overlays on the new volume
Map the old labels onto the new volume with
mris_apply_reg --src-label old/label/lh.your.label --streg
newsubject/surf/lh.white.old newsubject/surf/lh.white --o
newsubject/label/lh.your.label
On 11/3/2021 10:17 AM, Trisanna Sprung-Much wrote:
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Hi Doug
I did and I responded with the following:
that is correct Doug - the 2nd recon-all batch had a better set of scans
(intensity wise). For some reason the T1.mgz volumes are slightly translated
from one another, as are the surfaces (in that image I attached) and it is
creating the same issue with the labels when I use mri_label2label. Why would
mri_label2label with registration method as surface be having this issue? How
might I overcome this to avoid redrawing my labels?
Thank you,
Trisanna
--
Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, November 3, 2021 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2label issues
Did you see this response from a few days ago?
On 10/27/2021 11:26 AM, Douglas N. Greve wrote:
I'm not sure what you did or how to interpret that pic. If I understand, you
ran a case through recon-all and created labels on that case. You then
recon-all again using a totally different output where you improved the
homogeneity. You now want to map the labels you created on the 1st run to the
2nd run. Is that right?
On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:
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Hi there
I created labels on surfaces of subjects (chimp) registered to a particular
volumetric template. The labels were created on the surfaces in Freeview using
Freesurfer 7.1.
Since creating these labels, I improved the intensity inhomogeneity in the
scans and re-ran the surfaces. When I try to use mri_label2label to transpose
the labels to the new surfaces of each subject, the labels do not fall exactly
where they should. In fact, the surfaces themselves have a slight translation
in them (see snapshot). I assume this is because my registration to the
template that I did prior to running recon-all is differing somehow between the
2 groups. However, I thought that this should not matter since mri_label2label
--regmethod surface is using the sphere.reg to fsaverage.
I am wondering if there is anything I can do to improve mri_label2label to
avoid editing the labels manually?
Thank you for your time,
Trisanna
--
Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
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