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 <gr...@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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > 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. > > -- 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: wangl...@gmail.com
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