Re: [Freesurfer] Surface area of subcortical structures

, 2009 3:16 PM To: Douglas N Greve Cc: Elizabeth Selgrade; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Surface area of subcortical structures or use mri_extract_label instead of mri_binarize, like this, to get the left hippocampus: mri_extract_label aseg.mgz 17 lh

[Freesurfer] Surface area of subcortical structures

Hello, Is there a way to get the surface area of FreeSurfer subcortical structures? Thanks, Liz Selgrade ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes

abeth Selgrade Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes Hi Liz, what version are you using? Our newest longitudinal version removes this bias. cheers, Bruce On Mon, 31 Aug 2009, Elizabeth Selgrade wrote: > Hello FreeSurfer

[Freesurfer] Longitudinal vs. Cross-sectional Volumes

Hello FreeSurfer Users, I have been using the longitudinal stream to process four timepoints for about 20 subjects. I've extracted 9 ROIs and gotten their volumes for both the longitudinal segmentations and the cross-sectional segmentations. I'm noticing that there are seemingly significant diff

Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations

Martin, This works perfectly! Thanks, Liz -Original Message- From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Thursday, August 06, 2009 1:31 PM To: Elizabeth Selgrade Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Registering aseg to base for volume overlap

Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations

suggestions for what might be going on? Thank you! Liz -Original Message- From: Sita Kakunoori [mailto:s...@nmr.mgh.harvard.edu] Sent: Tuesday, August 04, 2009 12:33 PM To: Elizabeth Selgrade Cc: 'Martin Reuter'; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registerin

Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations

different tool that I should be using to apply the transform? Thank you for your help! Liz Selgrade -Original Message- From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Monday, August 03, 2009 5:28 PM To: Elizabeth Selgrade Cc: freesurfer@nmr.mgh.harvard.edu Subject:

[Freesurfer] Registering aseg to base for volume overlap calculations

Hello FreeSurfer Users, I am using the longitudinal stream to look at four timepoints/subject, and I'd like to transform all of my timepoints to the base scan's unbiased space so that I can calculate ROI volume overlap. I have been using tkregister2 to calculate the transform from my scan.base.lo

[Freesurfer] v.4.0.5 cross-sectional & v.4.4.0 longitudinal

Hello, Can I use v.4.4.0's longitudinal processing stream on scans that I cross-sectionally segmented with v.4.0.5? If so, do I need to rerun any steps of the cross-sectional processing before using these segmentations as inputs in the longitudinal processing? I know a similar question was alrea