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 TinaDid 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.
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