New subject: mris_divide_parcellation color table error (fwd)

30 May 2013

      Hi Tina
is this (attached) more what you wanted? If so, then I think you want to use 
mris_make_face_parcellation instead of mris_divide_parcellation. I can't 
remember what they used in that paper, but in mris_divide_parcellation I try to 
have the different units within a parcel have similar colors (which evidentally 
fails when you split it so finely)
Bruce
On Thu, 30 May 2013, Tina Jeon wrote:
...
I am running version 5.3- the latest version. I also tried running the codes 
on v5.0 and got the same result. Is there any way I can change the color 
table so that the colors of the parcellation are unique?
Thanks,
Tina
-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Wednesday, May 29, 2013 8:41 PM
To: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table error
Sure
On May 29, 2013, at 9:36 PM, Tina Jeon Tina.Jeon@utsouthwestern.edu wrote:
...
The colors are visually different by a shade then loop every 4 or so colors. 
I think the color table may be running on a loop? I can send the annot and 
surface file if you need that as well.
Best,
Tina

From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Wednesday, May 29, 2013 8:02 PM
To: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table error
p.s. can you send me the splittable text file ? I seem to have deleted
it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon
wrote:
...
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, "Bruce Fischl"
fischl@nmr.mgh.harvard.edu
wrote:
 Hi Tina

Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon Tina.Jeon@utsouthwestern.edu
wrote:
 Hello freesurfers,

 I am trying to create a figure similar to the Hagmann et
 al 2008  paper with 998 rois overlaid onto the surface,
 however, I am finding that there is no random, unique
 color for each parcellation unit like described in the
 help file for mris_divide_parcellation.

 I have attached a snapshot of my annotation file overlaid
 onto the surface, as you can see, the color iterates the
 same/similar color for a particular label. Can you tell me
 what I am doing wrong? Is there a pre-existing atlas as
 described in the Hagmann paper?

 My input:

 mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh
 ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010
 -03-25.gcs ./lh.aparc.998rois.annot

 mris_divide_parcellation subject_name lh
 ./lh.aparc.998rois.annot ./splittable.txt
 ./lh.annotation.998rois_26.annot

 Many thanks,

 Tina Jeon, MS

 UT Southwestern Medical Center ‘14

UT Southwestern Medical Center
The future of medicine, today.
 <neonate_buckner40_atlas.png>

 <splittable.txt>

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Re: [Freesurfer] mris_divide_parcellation color table error (fwd)