Thanks!
Yeah, I forgot this. Now, the results look right now.
Date: Thu, 25 Mar 2010 16:17:33 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Subject: RE: [Freesurfer] the thickness of manually selected vertex
are you sure you are using 1-based indices in matlab? Also, please post these to the list so that others can answer! On Thu, 25 Mar 2010, Guang Zeng wrote:
Using mris_anatomical_stats, I got
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 537 372 892 2.248 0.455 0.110 0.026 4 0.6 lh.mynew.label
I also calculate the average thickness of the vertices by loading the label file and thickness file into MATLAB, I got some numbers as: average cortical thickness: 2.2670 standard deviation: 0.5476
These numbers looks very close, are the difference caused by the partial volume?
Thanks! Guang
Date: Thu, 25 Mar 2010 15:52:34 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] the thickness of manually selected vertex
nope, mris_anatomical_stats will take either (with -l or -a I think) On Thu, 25 Mar 2010, Guang Zeng wrote:
Do I need convert the .label file to an annotation file before I run mris_anatomical_stats?
Could I get the same results if I do something like this:
- create the label file, and load it using MATLAB,
- find the corresponding ID of vertices I clicked.
- load .thickness file using matlab
- find the corresponding thickness value of these vertice
- compute the mean
Thanks!
Thank! Guang
Date: Wed, 24 Mar 2010 16:15:35 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the thickness of manually selected vertex
Q1: yes. Q2: do you want each of them individually or the average? You can save a label file of the 4 vertices and use mris_anatomical_stats to get the average
cheers Bruce
On Wed, 24 Mar 2010, Guang Zeng wrote:
Hi, there,
I have two questions about the ?h.thickness file.
If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness,
By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex.
Q1, Here, the value next to 'Curvature' is actually its thickness value, right? Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file?
Thanks! Guang
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