Thank you very much!

Kindly, I have one follow up question:

I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth" and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats".

I ran the following commands:

bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj

mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii

Are these stpes correct?

When I open T1.nii and the VOI.nii in freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback!

Best,
John

For version 6, it should not matter.

Sent: Friday, February 10, 2017 at 4:03 PM
From: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister

Hi John

one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
volume. I guess it might make the initialization less robust, not sure, but
I expect it works pretty well without doing brain extraction

cheers
Bruce

On Fri, 10 Feb 2017, John Anderson wrote:

> Hi FS experts,
> I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using
> the command
> bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
>
> do I need to apply brain extraction tools before this step or bb register
> can accept non-brain extracted images?
>
> Best,
> John
>
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