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