Dear Doug,
Thanks for your prompted answer, but I have another question about this. When I read the paper Kuperberg et al., Arch Gen Psychiatry 2003;60:878-888, I understand that in this paper, the authors computed the averaged surface. They then extracted ROIs from the average data and back-projected the ROIs to individual conformed space (Figure 2), followed by calculating mean cortical thickness of each ROI individually.
My questions are: 1) Can I be allowed to project the average paracellation (including subcortical and cortical surface) to fMRI data space using reg-feat2anat for extracting mean BOLD signal of each paracellation. Sorry for continuously bothering you about this confusing question to me.
2) Can you give me a further explanation about the means hidden under "Don't extract volumes, etc. If you want to use one of the surface parcellations, do a surface-based analysis."
All the best, Liang
2010/7/18 Doug Greve greve@nmr.mgh.harvard.edu
You can create a ribbon volume with the command below:
mris_volmask \ --label_left_white 2 --label_left_ribbon 3 \ --label_right_white 41 --label_right_ribbon 42 \ --save_ribbon --save_distance youraveragesubject
Note this when you make the aparc+aseg in this way, it should only be used when visualizing data on the mni305 brain. Don't extract volumes, etc. If you want to use one of the surface parcellations, do a surface-based analysis.
doug
On Sat, 17 Jul 2010, liang wang wrote:
Hi,
When I use make_average_subject to generate an average data, I can't find aparc.a2009s+aseg.mgz within the new average/mri. To get common parcellation to all subjects, I need to create this file. I understand that " mri_aparc2aseg --s average --a2009s " enable to perform what I want. However, when running this command, a error message shows up "ERROR: cannot find /drive3/Stammer/Thickness/average/mri/ribbon.mgz". As displayed by this message, I did not find the ribbon.mgz file. I don't konw how to figure out this problem. Any suggestions? By the way, my make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating.
Liang
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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