Yes it worked. Thank you that is exactly what I needed. Tina
-----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error (fwd) 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:fis...@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.j...@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 [fis...@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" >>> <fis...@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.j...@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> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> The information in this e-mail is intended only for the person to >>> whom it is addressed. If you believe this e-mail was sent to you in >>> error and the e-mail contains patient information, please contact >>> the Partners Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error but does not contain patient information, please >>> contact the sender and properly dispose of the e-mail. >>> >>> >>> >> <splittable.txt> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
