Hi Doug, Would your mri_segstats command work if instead of aseg.mgz, Sabin passed in the cerbellum parcellation in the same anatomical space as aseg?
--Thomas On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > After you run preproc-sess, there will be a file called register.dof6.dat. > Map fmri into the anatomical space, something like > > mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o > fmcpr.anat.nii.gz > > Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz > > However, I don't think that the aseg has those cerebellum parcellations. > > On 6/21/16 5:52 PM, Sabin Khadka wrote: > > 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 . 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