What is the problem with the orientation? The little letters indicate
that the orientation is correct. fslview ignores the orientation when
displaying so it might come out upside down.
On 07/05/2016 01:35 PM, Sabin Khadka wrote:
>
> Hi Doug, As you suggested I mapped fmri into the anatomical spa
Hi Sabin,
I think fslmeants should work. But you might need to first run
mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual
ROIs.
Also can you tell us which step generated the error "ERROR: must
specify a segmentation volume"? Is this the final step? Have you tried
overlaying Buck
Hi Thomas- On second thought is it valid to simply do if I want average
time series of the cerebellum regions?
fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
avgCerebellum.txt
Is this correct?
Cheers,
Sabin Khadka
On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka
wrote:
> Hi Th
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_vo
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_M
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
> wrote:
>> After you run pr
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
wrote:
> After you run preproc-sess, there will be a file called register.dof6.dat.
> M
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
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/b
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 ver
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 oddmri_segstats --annot fsaverage lh aparc --i
rest210/bold/001/fmcpr.odd.sm6.f
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.
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