Hi, I'm a beginner at handling MRIcron and nifti files. 

When I overay some image with a brain atlas image, It works correctly in the MRIcron.
But It doesn't work in the MRIcroGL correctly. 

I need to use the MRIcroGL. 
It's mainly because I can get a multi-sliced image only from the MRIcroGL. 
I can't get a "mosaic" image (e.g. 12x12 multi sliced axial image) from the MRIcron.

Anyway, I found that x,y,z axis of overlaid image wasn't matched with that of background image in the MRIcroGL.
I want to show you a one example. 

If you could help me, I would be grateful.
Thank you.

Can you share a copy of the background and overlay image. It is unclear if there is really a difference in the alignment or only in the thresholding and color scheme.

I tried to send email to "rorden @nospam@ sc.edu", but it doesn't work.
Please, could you let me know another your email address?
Then, I'll share my nifti hdr/img files.

Thank you

NITRC automatically adds bogus text into email addresses to block automatic spam harvesting. Therefore, if my email is actually "myname@sc.edu" then NITRC will display the email address as "myname @nospam@ sc.edu". Just reverse this convention to extract the email address.

Thanks for sharing your images. I note that one of your images appears to have been created by SPM2 (from 2002) or earlier, and uses the SPM-variant of the Analyze header. Please upgrade to SPM5 (from 2005) or later, which uses the NIfTI format. SPM used the Analyze format in a non-standard way, defining an origin. However, the origin had to be an integer, the image orientation could not be oblique to MNI space, and different versions of SPM made different assumptions regarding the left and right side. NIfTI provides an unambiguous solution for these problems. You can see how sparse the Analyze format representation is relative to NIfTI by examining the headers with fslhd:

fslhd w3T1_29214949_brain_final.hdr
fslhd 1Rlr.nii