Hello Freesurfer experts,
I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration.
Regards, Faezeh Vedaei
Hi Faezeh,
What do you mean by 3D brain map? Is it a 3D surface? What is the format of the ROIs you are trying to load?
Ruopeng
On 02/09/2016 02:01 PM, Faeze Vedaei wrote:
Hello Freesurfer experts,
I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration.
Regards, Faezeh Vedaei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Freesurfer experts,
In my project, I need to have a view of several specific ROIs which already specified after running re-con all based on Destrieux atlas. In this purpose, I tried to run mris_label2annot command to create ROIs in annot format to be viewed in Tksurfer by overlaying on pial surface (before this step, I created label files). In this process I got an error : need to specify color table file. I do not know how I can create and modify color table file here. May you guide me in this process to create color table and whether or not I have been following right steps? In advance, I'd appreciate your time and consideration.
Bests,
Faezeh Vedaei Research Associate CoGeNT Lab, Department of Neurology Michigan State University
On Tue, Feb 9, 2016 at 2:01 PM, Faeze Vedaei faezevedaei@gmail.com wrote:
Hello Freesurfer experts,
I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration.
Regards, Faezeh Vedaei
Run it with --help to get more info on the color table
On 02/18/2016 04:41 PM, Faeze Vedaei wrote:
Hi Freesurfer experts,
In my project, I need to have a view of several specific ROIs which already specified after running re-con all based on Destrieux atlas. In this purpose, I tried to run mris_label2annot command to create ROIs in annot format to be viewed in Tksurfer by overlaying on pial surface (before this step, I created label files). In this process I got an error : need to specify color table file. I do not know how I can create and modify color table file here. May you guide me in this process to create color table and whether or not I have been following right steps? In advance, I'd appreciate your time and consideration.
Bests,
Faezeh Vedaei Research Associate CoGeNT Lab, Department of Neurology Michigan State University
On Tue, Feb 9, 2016 at 2:01 PM, Faeze Vedaei <faezevedaei@gmail.com mailto:faezevedaei@gmail.com> wrote:
Hello Freesurfer experts, I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration. Regards, Faezeh Vedaei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Faeze Vedaei -
Ruopeng Wang