Nick,
The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used this cor to run the recon-all pipeline.
The original files could not be read by Freesurfer which is why I did that.
Also, this may be obvious to you but cannot the contrast be simply changed by Freesurfer. In tkmedit, the brightness and contrast can be adjusted so isn't there a way that recon-all can use this change while running the brain.
Thanks - Anil
On 2/14/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Anil,
The image has almost no contrast. I've attached a TIFF of one slice. How was this acquired? Bruce, any idea why it would be so white?
Nick
On Wed, 2007-02-14 at 16:10 -0500, aroy85@gmail.com wrote:
The following files have been uploaded to the Martinos Center FileDrop
site
by Anil Roy for you to download:
(1) orig.mgz
These files will expire in 30 days.
To view or download these files, go in your web browser to:
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc7...
DO NOT SHARE this web address with anyone else. It is your personal
access key to the files.
Overall Comment about files from Anil Roy:
Hi,
Attached is the orig.mgz file for the subject that quits at the
watershed step.
Thanks,
Anil.