yes, that looks right. The one question is about the fill threshold. You may
need to play with it a little to get a good looking ROI_2.nii (which should be
in registration with the functional -- but you should check it)
On 8/24/2019 2:56 PM, Rihana Rayan wrote:
External Email - Use Caution
Dear Dr. Greve,
Thank you so much for your prompt response.
I included your advice in the processing steps as bellow:
1- recon all
2- mri_binarize --i aparc.a2009s+aseg.mgz --o ROI.nii --match min max
3- bbregister --s --sub01 --mov meanfuctional.nii --initi-fsl --reg
register.dat
4- mri_label2vol --seg --ROI.nii --temp meanfuctional.nii --reg register.dat
--fillthresh 0.5 --o ROI_2.nii
I was wondering if you could check and verify the steps?
As another question is the ROI_2.nii coregistered with meanfunctional.nii?
Best Regards,
Rihana
On Fri, Aug 16, 2019 at 2:09 AM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
You shoul use mri_label2vol with ROI.nii as the --seg input. How do you
know that --regheader is right?
On 8/15/19 3:13 PM, Rihana Rayan wrote:
>
> External Email - Use Caution
>
> Dear FS users,
> I have performed recon-all on structural data and created ROIs (using
> mri_binarize), I want to mask functional data (GLM beta) with ROIs. To
> match the file sizes, I resampled the ROI.nii by performing the command:
> mri_vol2vol --mov ROI.nii --targ beta_01.nii --regheader --o
> ROI_in_beta.nii
> Multiplying ROI_in_mask.nii by GLM beta, results in NaN over some
> voxels. Can anyone help me solve the problem?
>
> Best regards,
> Rihana
>
>
>
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