Hi All,
I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and my goal is to have each label from aparc.a2009s.annot to fit that mask. How can I do this?
Thank you, Daiana
Hi Daiana
You should be able to use mri_vol2vol on the aparc+aseg.mgz and the talairach.xfm in the subject's mri/transforms dir.
cheers Bruce
On Thu, 9 Nov 2017, Daya P wrote:
Hi All, I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and my goal is to have each label from aparc.a2009s.annot to fit that mask. How can I do this?
Thank you, Daiana
Hi Bruce,
Can you give me some example code? I am not sure where the talairach would go?
On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daiana
You should be able to use mri_vol2vol on the aparc+aseg.mgz and the talairach.xfm in the subject's mri/transforms dir.
cheers Bruce
On Thu, 9 Nov 2017, Daya P wrote:
Hi All, I processed a bunch of subjects using recon-all, but now I would like to
get labels from
aparc.a2009s.annot from each subject in MNI space in nii from, the
problem is that the annotation
file (lh and rh) is in subject native space. I have a grey matter mask
in MNI from each subject and
my goal is to have each label from aparc.a2009s.annot to fit that mask. How can I do this?
Thank you, Daiana
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Hi Daiana
run mri_vol2vol --help. It has a bunch of examples and quite extensive help (thank you Doug!) Bruce
On Thu, 9 Nov 2017, Daya P wrote:
Hi Bruce, Can you give me some example code? I am not sure where the talairach would go?
On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Daiana
You should be able to use mri_vol2vol on the aparc+aseg.mgz and the talairach.xfm in the subject's mri/transforms dir. cheers Bruce On Thu, 9 Nov 2017, Daya P wrote: > Hi All, > I processed a bunch of subjects using recon-all, but now I would like to get labels from > aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation > file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and > my goal is to have each label from aparc.a2009s.annot to fit that mask. > How can I do this? > > Thank you, > Daiana > >
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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.
Hi all,
I am still struggling with my previous question
I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from. How can I obtain the Destrieux labels in nii format in MNI (2mm) How can I do this?
Thank you, Daiana
On Thu, Nov 9, 2017 at 1:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daiana
run mri_vol2vol --help. It has a bunch of examples and quite extensive help (thank you Doug!) Bruce
On Thu, 9 Nov 2017, Daya P wrote:
Hi Bruce, Can you give me some example code? I am not sure where the talairach
would go?
On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Daiana You should be able to use mri_vol2vol on the aparc+aseg.mgz and the talairach.xfm in the subject's mri/transforms dir. cheers Bruce On Thu, 9 Nov 2017, Daya P wrote: > Hi All, > I processed a bunch of subjects using recon-all, but now I wouldlike to get labels
from > aparc.a2009s.annot from each subject in MNI space in nii from,the problem is that the
annotation > file (lh and rh) is in subject native space. I have a greymatter mask in MNI from
each subject and > my goal is to have each label from aparc.a2009s.annot to fitthat mask.
> How can I do this? > > Thank you, > Daiana > >
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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
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
Sorry for the delay. First run mni152reg for each subject (should take only a few min, but needs FSL I think). Then run
mri_label2vol --aparc+aseg --temp MNI152_2mm.nii.gz --reg $SUBJECTS_DIR/subject/mri/transforms/reg.mni152.2mm.lta --o aparc+aseg.subject.mni152_2mm.nii.gz
On 11/14/2017 06:32 PM, Daya P wrote:
Hi all,
I am still struggling with my previous question
I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from. How can I obtain the Destrieux labels in nii format in MNI (2mm) How can I do this?
Thank you, Daiana
On Thu, Nov 9, 2017 at 1:36 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daiana run mri_vol2vol --help. It has a bunch of examples and quite extensive help (thank you Doug!) Bruce On Thu, 9 Nov 2017, Daya P wrote: > Hi Bruce, > Can you give me some example code? I am not sure where the talairach would go? > > > On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Daiana > > You should be able to use mri_vol2vol on the aparc+aseg.mgz and the > talairach.xfm in the subject's mri/transforms dir. > > cheers > Bruce > > On Thu, 9 Nov 2017, Daya P wrote: > > > Hi All, > > I processed a bunch of subjects using recon-all, but now I would like to get labels > from > > aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the > annotation > > file (lh and rh) is in subject native space. I have a grey matter mask in MNI from > each subject and > > my goal is to have each label from aparc.a2009s.annot to fit that mask. > > How can I do this? > > > > Thank you, > > Daiana > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Daya P -
Douglas N Greve