The easiest thing would be to run mri_segstats --annot subject lh yourannot --excludeid 0 --i fmc.odd.sm5.fsaverage.lh.nii.gz --avgwf avgwf.dat
avgwf.dat will have a row for each fmri time point and a column for each parcellation On 12/06/2018 01:45 PM, Zhi Li wrote: > > External Email - Use Caution > > Thank you for your kind reply. Sorry for the confusing question. Now I > have an annotation file in fsaverage space. And I want to extracted > mean time series from each roi in this annotation file from > preprocessed fMRI data, e.g. fmc.odd.sm5.fsaverage.lh.nii.gz. I think > the fcseed-config and fcseed-sess works when I input the volume data > such as fmc.odd.nii.gz, namely in the individual space. I have tried > transform this annotation file to the individual segmentation file, > however, the segmentation was wrong for each roi. May I ask if it is > available to extract time series from the surface data with the custom > annotation file in the fsaverage space? I am not clear if I could use > mri_segstats to achieve this, I found a example of this command in > individual space "mri_segstats --seg aseg-in-func.img --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --i func.img > --mask spmT.img --maskthresh 2.3 --sum bert.aseg-in-func.sum --avgwf > bert.avgwf.dat --avgwfvol bert.avgwf.img". How could I apply it into > the surface data? Any suggestions would be appreciated. > > Best wishes, > > Zhi > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
