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 _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:W...
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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Hello, Bruce,
Thanks a lot!
I think my new question is how to save a label file of the 4 vertices I selected.
Thanks! 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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Guang, Working in tksurfer, be sure to first do to Edit > Deselect Label and Edit > Unmark all Vertices just to make sure nothing else is chosen besides the 4 vertices you are interested in (unless you are sure that's all you have clicked on). Then click on the 4 vertices you want to mark. After you have chosen the last one, go to Tools > Labels > New Label from Marked Vertices. Then File > Label > Save Selected Label naming it whatever you want with the .label extension.
You can then run: mris_anatomical_stats -f blah.stats -l blah.label subjid lh
changing the hemi to whichever one you made the label on.
The resulting stats file should have 4 under NumVert otherwise it didn't work. Allison
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:
1. create the label file, and load it using MATLAB, 2. find the corresponding ID of vertices I clicked. 3. load .thickness file using matlab 4. find the corresponding thickness value of these vertice 5. 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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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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freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Bruce Fischl -
Guang Zeng