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.
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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto: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.edumailto: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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
hmmm, I haven't run that code in a long time. Are the colors different but not visually so? That is, do the rgb values differ by 1 or 2 or something like that? Or are they actualy identical?
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.
<neonate_buckner40_atlas.png> <splittable.txt> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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.
Tina, what version of FS are you using? At one point I fixed a bug that caused the color to be non-unique, but I don't think the problem looked that bad. If this is the program I fixed, then I'm pretty sure that it would have been in by 5.2. doug
On 5/29/13 9:01 PM, Bruce Fischl wrote:
hmmm, I haven't run that code in a long time. Are the colors different but not visually so? That is, do the rgb values differ by 1 or 2 or something like that? Or are they actualy identical?
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.
<neonate_buckner40_atlas.png> <splittable.txt> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Tina Jeon