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 <http://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
<mailto: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 <mailto: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 <http://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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