Can you send us the analyze files?
On Feb 24, 2011, at 12:37 PM, andrewkrause@ucla.edu wrote:
I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect).
-- Andrew
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Does it look like that when you load the original analyze into tkmedit?
andrewkrause@ucla.edu wrote:
Sure. Here's a screenshot of the orig.mgz.
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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