Hi Bruce,
I managed to do what I wanted: by linking the ?.aparc.annot file with ?thickness file and FreeSurferColorLUT.txt I get a list of thickness value, segID and structure name.
Now I can change each thickness into whatever value I want and save it as a curve file which I can then overlay on the pial surface. Thank you for your suggestions.
Ed
On 19 Jan 2011, at 17:31, Bruce Fischl wrote:
it's 'curv' format (read_curv.m I think) On Wed, 19 Jan 2011, Ed Gronenschild wrote:
What is the format of ?.thickness files?
On 19 Jan 2011, at 15:43, Bruce Fischl wrote:
read_annotation.m will load a .annot file. We'll try to digup the tksurfer bit that did this
On Wed, 19 Jan 2011, Ed Gronenschild wrote:
Hi Bruce,
I'm not familar with matlab but I can read the matlab scripts to understand what they are doing. I can then convert the code into C code. Which matlab script can I use to load the parcellation?
My suggestion would be to load the ?.thickness and replace the thickness values with the corresponding -log(p) values. However, I don't know which thickness in this file belongs to which segID?
Ed
On 19 Jan 2011, at 14:28, Bruce Fischl wrote:
Hi Ed,
sorry, I keep hoping someone else will respond as we did put something together to do this once upon a time, but apparently it's faded from all of our memories. You could do it in matlab by loading the parcellation and just setting every vertex with the parcellation value to the same scalar.
cheers Bruce
On Tue, 18 Jan 2011, Ed Gronenschild wrote:
Hi,
I've done some statistics on thickness and volume of the default cortical regions (segIDs 1000 - 1035 and 2000 - 2035) for a number of subjects. How can I show for instance the p values (expressed as -log(p)) as an overlay on the pial surface of fsaverage?
Ed
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glad it worked out
On Thu, 20 Jan 2011, Ed Gronenschild wrote:
Hi Bruce,
I managed to do what I wanted: by linking the ?.aparc.annot file with ?thickness file and FreeSurferColorLUT.txt I get a list of thickness value, segID and structure name.
Now I can change each thickness into whatever value I want and save it as a curve file which I can then overlay on the pial surface. Thank you for your suggestions.
Ed
On 19 Jan 2011, at 17:31, Bruce Fischl wrote:
it's 'curv' format (read_curv.m I think) On Wed, 19 Jan 2011, Ed Gronenschild wrote:
What is the format of ?.thickness files?
On 19 Jan 2011, at 15:43, Bruce Fischl wrote:
read_annotation.m will load a .annot file. We'll try to digup the tksurfer bit that did this
On Wed, 19 Jan 2011, Ed Gronenschild wrote:
Hi Bruce,
I'm not familar with matlab but I can read the matlab scripts to understand what they are doing. I can then convert the code into C code. Which matlab script can I use to load the parcellation?
My suggestion would be to load the ?.thickness and replace the thickness values with the corresponding -log(p) values. However, I don't know which thickness in this file belongs to which segID?
Ed
On 19 Jan 2011, at 14:28, Bruce Fischl wrote:
Hi Ed,
sorry, I keep hoping someone else will respond as we did put something together to do this once upon a time, but apparently it's faded from all of our memories. You could do it in matlab by loading the parcellation and just setting every vertex with the parcellation value to the same scalar.
cheers Bruce
On Tue, 18 Jan 2011, Ed Gronenschild wrote:
> Hi, > > I've done some statistics on thickness and volume > of the default cortical regions (segIDs 1000 - 1035 > and 2000 - 2035) for a number of subjects. > How can I show for instance the p values > (expressed as -log(p)) as an overlay on the pial > surface of fsaverage? > > Ed > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Ed Gronenschild