You don't need to do the bbregister or tkregister steps if the FS results are based on the T1.nii image as input. You can just use mri_vol2vol with --regheader instead of --reg t1.reg.dat (but the results should be about the same).
For the problem, does aparc+aseg show up properly on the T1.nii? what is your freeview command line?
On 02/14/2017 01:54 PM, John Anderson wrote:
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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