I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag.
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 10:10 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug
On 11/3/14 9:44 AM, Smith, Michael wrote: Hi Doug,
We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way?
Best,
Michael S.
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, November 3, 2014 at 9:31 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug
On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance!
It is worth noting I am running Darwin-lion-stable-pub-v5.3.0
Best,
Michael S.
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