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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