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
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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For version 6, it should not matter.
On 2/10/17 3:59 PM, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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John Anderson