Hi Doug, thanks. Hi Sabin, you can use the following steps to transform the Buckner cerebellum atlas to your subject's native anatomical space and then follow Doug's instructions (taken and adapted from another user Bronwyn's email):
1. Run MNI152 1mm template through recon-all recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer nonlinear volumetric space mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o BucknerAtlas1mm_FSI.nii.gz --nearest 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear volumetric space to each subject: mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph 4. Create a cerebellum gray matter mask in the native subject's space by applying mri_binarize to aparc+aseg.mgz of the subject mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o cerebellum_mask_subjID.nii.gz 5. Using this mask to mask the Buckner cerebellum parcellations fslmaths Buckner2011_atlas_subjID.nii.gz -mas cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz Regards, Thomas On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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
