Hi all,
I'd like to convert SPM2 spmT files to FreeSurfer space. I have a Colin template brain available to help with the conversion, as well. Has anyone done this before? Any suggestions on how to do this?
Many thanks in advance, Eun Young
what space is the spmT volume in?
On 11/15/2012 04:58 PM, Eun Young Choi wrote:
Hi all,
I'd like to convert SPM2 spmT files to FreeSurfer space. I have a Colin template brain available to help with the conversion, as well. Has anyone done this before? Any suggestions on how to do this?
Many thanks in advance, Eun Young
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
It's in MNI space.
Thanks, Eun Young
On Mon, Nov 19, 2012 at 11:05 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
what space is the spmT volume in?
On 11/15/2012 04:58 PM, Eun Young Choi wrote:
Hi all,
I'd like to convert SPM2 spmT files to FreeSurfer space. I have a Colin template brain available to help with the conversion, as well. Has anyone done this before? Any suggestions on how to do this?
Many thanks in advance, Eun Young
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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If it is in mni152 space, you can use $FREESURFER_HOME/average/mni152.register.dat doug
On 11/19/2012 12:12 PM, Eun Young Choi wrote:
Hi Doug,
It's in MNI space.
Thanks, Eun Young
On Mon, Nov 19, 2012 at 11:05 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what space is the spmT volume in? On 11/15/2012 04:58 PM, Eun Young Choi wrote: > Hi all, > > I'd like to convert SPM2 spmT files to FreeSurfer space. I have a > Colin template brain available to help with the conversion, as well. > Has anyone done this before? Any suggestions on how to do this? > > Many thanks in advance, > Eun Young > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Dear list, I am quite new in the use of freesurfer and I have two doubts.
1. I am studying the visual areas of the brain, but I do not know how to perform a vertex analysis within a ROI. I already know how to obtain thickness data on a ROI (either drawn by hand or labeled), but I would like to restrict the area of a vertex-analysis to my ROI (visual brain areas)
2. When performing a vertex-analysis, is it correct to include TIV (total intracranial volume) as a nuisance variable?
Thank you for any help
Angela
Angela Favaro, MD, PhD Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy
On 11/19/2012 12:28 PM, angela.favaro@unipd.it wrote:
Dear list, I am quite new in the use of freesurfer and I have two doubts.
- I am studying the visual areas of the brain, but I do not know how to
perform a vertex analysis within a ROI. I already know how to obtain thickness data on a ROI (either drawn by hand or labeled), but I would like to restrict the area of a vertex-analysis to my ROI (visual brain areas)
When you run mri_glmfit, you can pass it a label (--label) or mask (--mask) in which you specify only the areas you want to analyze. You will need to re-run the simulation for the correction for multiple comparisons since your search space has changed.
- When performing a vertex-analysis, is it correct to include TIV (total
intracranial volume) as a nuisance variable?
It depends on what you are analyzing. I think for thickness, people are not doing a correction. For volume, they are. For surface, a correction is often done, but not with the raw TIV (maybe taking the 2/3 root to give it surface dimensions). doug
Thank you for any help
Angela
Angela Favaro, MD, PhD Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy
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