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 greve@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)?
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. >>> >>> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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