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 greve@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 <greve@nmr.mgh.harvard.edu mailto: greve@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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
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