Dear Doug, Thanks. According to your suggestions, I would extract fmri time course from an individual paracellation with subcortical regions (e.g. caudate, thalamus...). Would you like to help me to make sure whether the following commands are correct. Here the filtered_fun_data.nii.gz did not be smoothed. Thanks a lot.
reg-feat2anat --feat SUBID/bold.feat --subject SUBID aseg2feat --feat SUBID/bold.feat --aseg aparcs+aseg mri_segstats --seg SUBID/bold.feat/reg/ freesurfer/aparc.a2009s+aseg.nii.gz --in filtered_fun_data.nii.gz -avgwf file.dat Liang 2010/7/19 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > mapping the time courses to the average subject does not solve this > problem, it just hides it. I'm not sure why this would be of a concern > anyway. There might be a tiny difference in the expected variance for each > subject, but, unless the region is very small, the differences won't amount > for much. > > doug > > liang wang wrote: > >> Dear Doug, >> >> Thanks for your comments. However, I am worried about the different number >> of voxels within each parcellation between subjects, if extracting fmri time >> course from individual parcellation result. >> >> Also, I am using the following combined commands to carry out the steps. >> Do you think it's correct? >> reg-feat2anat --feat SUBID/bold.feat --subject SUBID >> aseg2feat --feat SUBID/bold.feat --aseg aparcs+aseg >> mri_segstats --seg SUBID/bold.feat/reg/freesurfer/aparc.a2009s+aseg.nii.gz >> --in filtered_fun_data.nii.gz -avgwf file.dat >> >> Thanks, >> Liang >> >> 2010/7/18 Doug Greve <gr...@nmr.mgh.harvard.edu <mailto: >> gr...@nmr.mgh.harvard.edu>> >> >> >> >> definitely use the individuals. Use mri_vol2surf to convert the motion >> corrected (and otherwise unsmoothed) fmri time courses to the >> surface. Then use mri_segstats with the --avgwf and --annot options >> to compute the mean time course over the parcellations. >> >> doug >> >> >> >> >> On Sat, 17 Jul 2010, liang wang wrote: >> >> Hi, >> >> Does anyone know one of studies which uses the parcellations >> (aparc or >> aparc.a2009s) Freesurfer provides to extract fMRI time course >> from each >> subject's fMRI data. Reading the instructions in Freesurfer >> Wiki, I know how >> to do that. However, I am not sure whether I should use the >> parcellations >> from the average output (obtained from make_average_subject), >> or the >> parcellations based on each subject. I would next compute >> functional >> connectivity between these regions. I am appreciated for any >> suggestions. >> >> Liang >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 <mailto:wangl...@gmail.com> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > 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 > > -- 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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