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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External Email - Use Caution
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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Wednesday, November 3, 2021 11:08 AM
*To:* freesurfer@nmr.mgh.harvard.edu <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:
External Email - Use Caution
External Email - Use Caution
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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