Hi,
My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when finding its loss in the ?h.aparc.stats file. For all subjects, I did not find any morphometric measures of this region.
Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown.
I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much.
Liang
liang wang wrote:
Hi,
My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when finding its loss in the ?h.aparc.stats file. For all subjects, I did not find any morphometric measures of this region.
The CC is a volume structure and so it is reported in the aseg.stats file (it is in the aparc for convenience).
Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown.
What is where the insula should be?
doug
I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much.
Liang
-- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit@gmail.com mailto:wanglbit@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi
Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown.
What is where the insula should be?
I think that the insula should be displayed in the ?h.aparc.annot, because ?h.aparc.stats reports several surface measurements of this regions. But I can't find it.
Liang
Hi Doug,
Maybe I can't give clear information about my problem in the previous post. Please allow me report it again. My question is that I can't find the insula in the averaged ?h.aparc.annot obtained from the command make_average_surface. I check ?h.aparc.annot of each subject and find existence of the insula inside each subject's file. I don't know what's the wrong during the average process. I am looking forward to your suggestions. Thanks.
Liang
2010/7/13 liang wang wanglbit@gmail.com
Hi
Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown.
What is where the insula should be?
I think that the insula should be displayed in the ?h.aparc.annot, because ?h.aparc.stats reports several surface measurements of this regions. But I can't find it.
Liang
-- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit@gmail.com
Liang,
make_average_surface is not using the latest atlas when creating the .annot files. i've attached a fixed version of make_average_surface which you should copy to your $FREESURFER_HOME/bin directory.
n.
On Thu, 2010-07-15 at 14:36 -0700, liang wang wrote:
Hi Doug,
Maybe I can't give clear information about my problem in the previous post. Please allow me report it again. My question is that I can't find the insula in the averaged ?h.aparc.annot obtained from the command make_average_surface. I check ?h.aparc.annot of each subject and find existence of the insula inside each subject's file. I don't know what's the wrong during the average process. I am looking forward to your suggestions. Thanks.
Liang
2010/7/13 liang wang wanglbit@gmail.com Hi
Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown. What is where the insula should be? I think that the insula should be displayed in the ?h.aparc.annot, because ?h.aparc.stats reports several surface measurements of this regions. But I can't find it. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit@gmail.com-- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit@gmail.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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