To check whether the orientation is correct, you can view it in freeview or tkmedit. When you click on the axial view it should show up axially, etc. Though you cannot tell whether it is left-right reversed this way. You cannot feed it a matrix, but you can specify the direction cosines on the mri_convert command line (-iid, -ijd, -ikd). You'll have to play with it a bit. You can also try giving it an orientation string instead. if you run mri_convert without any options, then it will give you lots of documentation.

On 3/20/16 8:44 PM, Reema Jayakar wrote:
Hello FS list subscribers,

Is there a way to manually feed FS with NIfTI-1 qform or sform information? Or correctly add this information to the original .nii files? My sense of the problem is that there is a problem with the header information in my .nii files and FS cannot tell what is anterior, posterior, left, right. 

That said, I am very new to FS and my interpretation of the error could be wrong. So I am laying out the details below (recon-all.log is also attached to this email):
  • When I try to run recon-all there are no output images/files generated and the message I get is that the Talairach transform failed 
  • When I try to run autorecon1 an autorecon2 with the "-notal check" flag, FS does not give me any error message and proceeds with generating output. However, I can visually see (via brainmask.mgz) that oreintations are messed up (e.g., tried to register coronal orientation on top of sagittal orientation)
  • This problem only occurs with .nii files from a particular study that came out of a specific scanner. All my other data are running through FS smoothly, which is why I think there is some problem with the .nii files
  • Also, when I view my raw .nii images in FSL view none of the usual orientation markers are visible to me, which again suggest that they may be missing?
  • Unfortunately, I do not currently have the original .dcm files available as this is a multi-site archival study

Any help you can provide to resolve this issue would be really appreciated! 

Thank you,
Reema



--
Reema Jayakar, M.A.
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University



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