Hi Doug,

Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from Buckner 2011 7 Cerebellar network. Please see below for the steps I performed to extract time series from Buckner 2011 7 Cerebellar networks. If you could give your thoughts on the steps/process that'd be great.

*1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all Yeo2011_MNI152_FS

*2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfe nonlinear volumetric space* 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

*3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear* volumetric space to each subject: 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

*4. Create a cerebellum gray matter mask in the native subject's space by applying mri_binarize to aparc2009s+aseg.mgz of the subject*

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --o cerebellum_mask_FSSub_m8.nii.gz # For left mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o cerebellum_mask_FSSub_m47.nii.gz # FOr right

*5. Using this mask to mask the Buckner cerebellum parcellations*

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8.nii.gz # For left fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47.nii.gz # For right

*6. Functional data to anatomical space*

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz # functional into anatomical space

*7. Extract L/R Cerebellar ROIs time series*

mri_segstats --seg {analysisrootdir}/analysis/Buckner_atlas_FSSub_m8.nii.gz --ctab $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt # extract Left Cerebellum time series mri_segstats --seg {analysisrootdir}/analysis/Buckner_atlas_FSSub_m47.nii.gz --ctab $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt # extract right Cerebellum time series

Cheers, Sabin Khadka

On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

has this question been answered?

On 06/17/2016 09:42 AM, curry_sam77@yahoo.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.

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