It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)?
andrewkrause@ucla.edu wrote:
Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip
-- Andrew
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 >> >> >> 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. >> >> > > >
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