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 <gr...@nmr.mgh.harvard.edu>: > Does it look like that when you load the original analyze into tkmedit? > > andrewkra...@ucla.edu wrote: >> Sure. Here's a screenshot of the orig.mgz. >> >> Quoting Bruce Fischl <fis...@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, 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 >>> >> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > gr...@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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
