Can you send us an image? The 16 bit shouldn't be a problem Bruce
On Feb 23, 2011, at 7:28 PM, andrewkra...@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 <fis...@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, andrewkra...@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
