yes
On 6/24/16 9:19 AM, Thomas Yeo wrote: > 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 . 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 >> >> >> >> _______________________________________________ >> 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 >> >> >> 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
