1. Segmentation of partial brain
Dear FreeSurfers,
1. Can I expect recon-all to work on a T1W image where only part of the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail.
Thank you,
---------------------- 2. Rotated segmentation
Dear FreeSurfers,
I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt?
Thank you,
On 08/19/2013 12:42 PM, Liane Hunter wrote:
- Segmentation of partial brain
Dear FreeSurfers,
- Can I expect recon-all to work on a T1W image where only part of
the brain is in FOV? The obvious answer is that I should just try, but it would help to know in case I get unexpected results. Perhaps a more appropriate question is: what should I expect to work and what should I expect to fail.
I doubt it will work. I the regsitrations will likely fail.
Thank you,
- Rotated segmentation
Dear FreeSurfers,
I start with a T1W image in NIFTI format. After running recon-all, I use mri_convert to convert aseg.mgz to aseg.nii. This aseg.nii image does not overlay the original T1W. It is slightly rotated. Is it normal? If I would like to make it overlay what should I do? Register using flirt?
See this page http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Thank you,
Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Liane Hunter