you can use
mri_convert -rl ...
to reslice the output of bet so that it has the same geometry as the rest of our stream
cheers Bruce
On Wed, 6 Mar 2013, Winter, Warren wrote:
Hi again, We have had some suboptimal results from FreeSurfer's skullstripping algorithm, even after iteratively trying different watershed thresholds and after checking the quality of Talairach registration. The results are pretty good, but often leave some dura matter and bits of neck behind whose higher intensity values, I believe, may end up skewing recon-all's later estimation of the range of intensity values within grey matter, and consequently compromising the accuracy of pial surface estimation.
FSL's BET, however, seems to do a better job of extracting the brain, at least for our dataset. So, I was wondering if I might be able to skip over mri_watershed and feed autorecon2 and autorecon3 a brainmask.mgz file created using BET. I tried this procedure:
- mri_convert <path/to/T1dcm> T1.nii.gz
- bet T1.nii.gz BET_brainmask.nii.gz -A
- mri_convert BET_brainmask.nii.gz BET_brainmask.mgz
- recon-all -s <subjid> -autorecon1 -noskullstrip
- mv BET_brainmask.nii.gz ./<subjid>/mri/brainmask.mgz
- recon-all -s <subjid> -autorecon2 -autorecon3
And I got this error message, right after normalization2:
" #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_bet/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 "
I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match those of brainmask.mgz, resulting during normalization2 in a mismatch between brain.mgz and brainmask.mgz. Does that seem right, and is there a possible workaround?
Thank you!
Warren
-- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224