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 <ythomas@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.sabinkhadka@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
>

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