That looks right, though mri_segstats might want a summary file. If so , just added --sum junk
doug liang wang wrote: > 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 > <mailto: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> > <mailto: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> > <mailto: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> > <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> > <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> > <mailto:wangl...@gmail.com <mailto:wangl...@gmail.com>> > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <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> > > > > > -- > 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> -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
