Hi Sabin, I think fslmeants should work. But you might need to first run mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual ROIs.
Also can you tell us which step generated the error "ERROR: must specify a segmentation volume"? Is this the final step? Have you tried overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in freeview to check that the previous steps have worked? Thanks, Thomas On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka <mr.sabinkha...@gmail.com> wrote: > Hi Thomas- On second thought is it valid to simply do if I want average time > series of the cerebellum regions? > > fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> > avgCerebellum.txt > > Is this correct? > > > Cheers, > Sabin Khadka > > On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka <mr.sabinkha...@gmail.com> > wrote: >> >> Hi Thomas and Doug- >> >> Thanks for you suggestions. Per your suggestions I performed following >> >> recon-all -i >> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz >> -subjid Yeo2011_MNI152_FS >> >> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS >> >> mri_vol2vol --mov >> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz >> \ >> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z >> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest >> >> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ >> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o >> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph >> >> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o >> cerebellum_mask_FSSub.nii.gz >> >> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz >> Buckner_atlas_FSSub >> >> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o >> fmcpr.anat.nii.gz >> >> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf >> test.txt >> >> However, I got the following error >> ERROR: must specify a segmentation volume >> >> Am I doing anything wrong here. Do you have any suggestions/fixes? >> >> >> Cheers, >> Sabin Khadka >> >> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote: >>> >>> 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. 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