Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I process my fmri data with
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd and then to extract ROI time series values I did 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 Now I am not sure as how to extract cerebellum ROIs (time series as described in Buckner et.al 2011)? If there are any other additional steps I need to perform ? or if I have to use some other scripts commands (other than mri_segstats). Cheers, Sabin Khadka On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote: > 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 >
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