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.
can you tell us the details of the acquisition? The contrast is intrinsic, and it has to be sufficient for g/w segmentation.
On Wed, 14 Feb 2007, Anil Roy wrote:
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.
Anil,
On this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
there is a TIFF image of some example scans having decent contrast.
Nick
On Wed, 2007-02-14 at 17:03 -0500, Bruce Fischl wrote:
can you tell us the details of the acquisition? The contrast is intrinsic, and it has to be sufficient for g/w segmentation.
On Wed, 14 Feb 2007, Anil Roy wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Anil,
I was able to successfully run -autorecon1 (after performing my own tal alignment). This included the skullstrip.
How much memory does your machine have? It needs to have at least 2GB.
Nick
On Wed, 2007-02-14 at 15:49 -0600, Anil Roy wrote:
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/5010/426/7389dc72a7ad03d19b7736c8a7adff69 > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu