Hi Doug, As you suggested I mapped fmri into the anatomical space using
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz
The orientation of fmcpr.anat.nii.gz seem to have some problem (see below). However the label seems to be correct. I am a bit confused here. Do I need to tranform the file somehow?
fmcpr.nii.gz
[image: Inline image 1]
fmcpr.anat.nii.gz
[image: Inline image 2]
Cheers, Sabin Khadka
On Thu, Jun 23, 2016 at 11:28 AM, Douglas Greve greve@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 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.commr.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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