Hi,
We want to compare grey matter volumes from specific labels. Is the output of mris_anatomical_stats normalized in any way? It doesn't appear to be.
Thanks!
+glenn
you mean by ICV? No, although in our new versions we compute ICV/TIV. Do you mean volume labels or surface labels? Volume of volume labels can be computed with mri_label_volume, surfaces can be given to mris_anatomical_stats -l <label name>
cheers, Bruce
On Thu, 8 Dec 2005, Glenn Lawyer wrote:
Hi,
We want to compare grey matter volumes from specific labels. Is the output of mris_anatomical_stats normalized in any way? It doesn't appear to be.
Thanks!
+glenn
Hi all, I would like to create my own custom parcellation atlas for the frontal lobes using labels that I have traced on the surfaces. From what I can gather from the mailing list, I need to use mris_ca_train to do this. The usage states indicates I need to specify a canonical surface and an annotation file, but I don't know how to create these. Also, I would have thought I would need to input one annotation file per subject, rather than the single one that is implied in the usage. Do need to do something else before I start using mris_ca_train? Any help is much appreciated. Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
you need 1 annot/training subjects. The canonical surface is the ?h.sphere.reg. The annots can be created by drawing in tksurfer.
cheers, Bruce
On Sat, 10 Dec 2005, Fornito, Alexander wrote:
Hi all, I would like to create my own custom parcellation atlas for the frontal lobes using labels that I have traced on the surfaces. From what I can gather from the mailing list, I need to use mris_ca_train to do this. The usage states indicates I need to specify a canonical surface and an annotation file, but I don't know how to create these. Also, I would have thought I would need to input one annotation file per subject, rather than the single one that is implied in the usage. Do need to do something else before I start using mris_ca_train? Any help is much appreciated. Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, do you mean 1 annot per subject in the training set? I noticed that there is an 'export annotation' option in tksurfer. I figured it would be a matter of drawing my labels on each subject, then, while they're all loaded, clicking the 'export annotation' option and saving the file. However, if I do this and then try to load the annotation again, nothing appears. Am i missing something? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sun 11/12/2005 12:34 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Custom parcellation atlas
you need 1 annot/training subjects. The canonical surface is the ?h.sphere.reg. The annots can be created by drawing in tksurfer.
cheers, Bruce
On Sat, 10 Dec 2005, Fornito, Alexander wrote:
Hi all, I would like to create my own custom parcellation atlas for the frontal lobes using labels that I have traced on the surfaces. From what I can gather from the mailing list, I need to use mris_ca_train to do this. The usage states indicates I need to specify a canonical surface and an annotation file, but I don't know how to create these. Also, I would have thought I would need to input one annotation file per subject, rather than the single one that is implied in the usage. Do need to do something else before I start using mris_ca_train? Any help is much appreciated. Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fornito, Alexander -
Glenn Lawyer