not an easy way. You'd have to find out what the byte swapping is in each file (or verify that the byteswapping is different). The other programs may check that the voxel values are "reasonable" and byteswap them if they are not.
andrewkra...@ucla.edu wrote: > There's actually quite a large chance for that, as we convert the > DICOMs to ANALYZE on iMacs; skull-strip mostly on PCs; register and do > other processing on remote machines running OpenBSD, IRIX, and Linux > (some of which are little-endian and some of which are big-endian); > and then check everything and do stats locally on the Macs. > > When I look at the ANALYZE image in BrainSuite and Shiva (two programs > from LONI), they look fine, but I don't know if they're treating the > headers differently than other viewers. Is there a way to check > besides just how it looks? > > -- Andrew > > Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > >> 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 >> >> > > > _______________________________________________ > 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
