This is a question for Ruopeng (who is the author of freeview, and
cc'ed). Can you upload the subject and the annot file so that he can
replicate the problem?
doug
On 04/03/2014 06:55 PM, Laura Taylor wrote:
> Hi Again Doug,
>
> I was able to get what I was looking for after I modified my ctab
Try excluding the following line from your ctab
0 Unknown 0 0 00
The list in the ctab should match that of the labels you are passing on
the command line (it is ok to have more in the ctab than on the command
line)
doug
On 04/02/2014 01:05 PM, Laura Taylor
Hi Shantanu,
Thanks for your reply. My command line in tksurfer was:
~$ tksurfer TGT_N61AvgSubject rh inflated -annotation
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_Apr3.annot
You can also do the same for the pial surface.
The original ctab file (r/lh.aparc.a
Hi Laura,
I am facing the same problem when using freeview. Can you tell me what was
your commandline that solved the problem in tksurfer? How did you get the
ctab 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 am
hoping, however, that it is still possible to get things to work in
freeview.
For the ctab file, I put my 6 parcellated ROI's at the st
Hi Doug,
Thank you for your reply.
This was my mris_label2annot command line:
woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
--a Comp2RH_TGTN61_properGreyRH --l
/Data/freesurfer/subjects/TGT
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, creating a
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
black
