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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html