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)?
andrewkra...@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 <fis...@nmr.mgh.harvard.edu>: > >> Can you send us the analyze files? >> >> >> >> On Feb 24, 2011, at 12:37 PM, andrewkra...@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 <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 >>>> >>>> >>> >>> >>> >> > > > -- 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
