Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix)
The machine has 4 gigs of RAM. Also, AFNI is able to talairach and skull strip. Is there a way I can input the files from AFNI to Freesurfer to resume the recon-all pipeline.
Nick, is there a way for me to see your reg so that I can be sure that its not my created xfm that is causing this problem.
Thanks,
Anil.
On 2/14/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
why is the background so high? Also, what field strength was this at? There looks to be dielectric-like center brightening. The contrast isn't terrible though.
On Wed, 14 Feb 2007, Nick Schmansky wrote:
Bruce,
the orig.mgz can be downloaded via the filedrop, see link in email below.
or i have copied it to:
/autofs/space/minerva_001/users/nicks/subjects/anil/mri
N.
On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl wrote:
put the .mgz somewhere and I'll take a look. And make sure it's the orig.mgz, which is un-normalized
On Wed, 14 Feb 2007, Nick Schmansky 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.
Also, I ran it on a Red Hat system and I'm still getting the error so I don't think it is a machine specific problem. Any suggestions.
Thanks. Anil.
On 2/14/07, Anil Roy aroy85@gmail.com wrote:
Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix)
The machine has 4 gigs of RAM. Also, AFNI is able to talairach and skull strip. Is there a way I can input the files from AFNI to Freesurfer to resume the recon-all pipeline.
Nick, is there a way for me to see your reg so that I can be sure that its not my created xfm that is causing this problem.
Thanks,
Anil.
On 2/14/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
why is the background so high? Also, what field strength was this at? There looks to be dielectric-like center brightening. The contrast isn't terrible though.
On Wed, 14 Feb 2007, Nick Schmansky wrote:
Bruce,
the orig.mgz can be downloaded via the filedrop, see link in email below.
or i have copied it to:
/autofs/space/minerva_001/users/nicks/subjects/anil/mri
N.
On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl wrote:
put the .mgz somewhere and I'll take a look. And make sure it's the orig.mgz, which is un-normalized
On Wed, 14 Feb 2007, Nick Schmansky 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.
freesurfer@nmr.mgh.harvard.edu
-
Anil Roy