Hi Sabin, The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical substructures of the cerebellum (e.g., Crus I, etc). Is that what you want? Or are you looking to use the functional parcels defined in Buckner 2011?
In addition, I do not know how mri_segstats works, so I cannot verify how you call the command is correct. Maybe others can provide feedback here. However, the Buckner cerebellar parcellations in $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152 space. From your command, I assume your data is in MNI305 space. So you might need to transform the parcellation from MNI152 to MNI305. Thanks, Thomas On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka <mr.sabinkha...@gmail.com> wrote: > Hi all, > > I am trying to extract mean time series BOLD data using FSFAST from Cortical > ROIs + sub cortical ROIs and cerebellum. > > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 > -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt > mri_segstats --annot fsaverage rh aparc --i > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt > > and for cortical time series > > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf > subCorticalTimeSeries.txt > > But I am not sure on how exactly to extract time series from cerebellar > regions. So if I want to extract time series from regions as described in > Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in > FreeSurferCololLUT.txt? If not could you please direct me to processes that > I can use. > > Cheers, > Sabin Khadka > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
