Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkrause@ucla.edu wrote:
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size?
Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check.
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
add the flag -notal-check to the end of recon-all command to skip the check.
if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
n.
On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.
When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error
"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.
Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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