Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

file and did you edit it using the RGB color codes? Thanks in advance. Shantanu On Thu, April 3, 2014 6:55 pm, Laura Taylor wrote: Hi Again Doug, I was able to get what I was looking for after I modified my ctab file slightly and used tksurfer instead of freeview to display the images. I

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

it would be possible to display these images properly in freeview as well? Thank you very much for your time, Laura On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor taylor.cnos@gmail.comwrote: Hi Doug, Thank you for your reply. This was my mris_label2annot command line: woodward@Bambi

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

: What was your mris_label2annot command line? What was the terminal output? Can you send the colortable file you passed with --ctab? doug On 04/01/2014 02:25 PM, Laura Taylor wrote: Hello, I have run mri_annotation2label and then selected the labels corresponding to my ROI

[Freesurfer] displaying annotations on inflated brain in freeview

Hi, I'm having trouble displaying annotations on inflated brains in freeview. I have loaded and selected the inflated surface and annotation for that subject, but nothing shows up on the brain. I have had no trouble displaying annotations on the pial surface of the brain. Thank you for your

[Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

Hello, I have run mri_annotation2label and then selected the labels corresponding to my ROI, creating a new annotation file using mris_label2annot. When I load my new annotation file in freeview, the ROI's are displayed nicely in different colors. However the remainder of the brain is dark

[Freesurfer] Displaying ROI's from Destrieux atlas (aparc.a2009s)

Hi there, I am looking to somehow display a handful of cortical areas from the Destrieux atlas (aparc.a2009s). Is there a way to do this? Thanks, Laura ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Fwd: Problems dipslaying annotations in freeview

On Tue, Dec 17, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: So when you say you cannot load it, what do you mean? doug On 12/17/2013 02:55 PM, Laura Taylor wrote: Hi Douglas, I checked the status

Re: [Freesurfer] Problems dipslaying annotations in freeview

the right hemisphere and is tye-died in appearance. Thanks, Laura On Tue, Dec 17, 2013 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: So when you say you cannot load it, what do you mean? doug On 12/17/2013 02:55 PM, Laura Taylor wrote: Hi Douglas, I checked

Re: [Freesurfer] Problems dipslaying annotations in freeview

(and it appears on the correct hemisphere). Can you help at all with this? Thank you, Laura On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor taylor.cnos@gmail.comwrote: Hi, yes thank you both. That is exactly what the problem was. Laura On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve gr

Re: [Freesurfer] Problems dipslaying annotations in freeview

? Did recon-all complete properly? doug On 12/17/2013 01:35 PM, Laura Taylor wrote: Hi again, Douglas and freesurfer experts. Unfortunately my problem cannot be explained by having made manual edits and then not finishing recon-all. When I load subjects that I did not manually edit, I am

Re: [Freesurfer] Problems dipslaying annotations in freeview

making manual edits and then not finishing a re-run of recon-all. Chris On 12/10/2013 02:00 PM, Laura Taylor wrote: Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot under the annotations

Re: [Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory

to visualize. It included your home dir in the path probably because that was your pwd. cheers Bruce On Wed, 27 Nov 2013, Laura Taylor wrote: Hi, I previously installed set-up and have successfully used freesurfer to run recon-all and visualize my results in tkmedit and tksurfer. However

[Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory

Hi, I previously installed set-up and have successfully used freesurfer to run recon-all and visualize my results in tkmedit and tksurfer. However when I went to analyze my data and also view it in freeview I have run into a problem with what my home directory is considered for these

[Freesurfer] command not found - unable to set up freesurfer

Hi, I have just downloaded and I thought installed freesurfer on a Debian system (Debian 3.2.51-1 x86_64 GNU/Linux). However when I go to test the install by typing in freeview (or any other command) in the terminal window I get the following: % freeview freeview: Command not found. Before