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> > > 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 > 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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