We are trying to reconstruct our functional MRI images using AFNI but we’re receiving the error below. The error does not occur when we try to reconstruct anatomical images.
ERROR: Failed to handle oblique (tolerance exceeded). Sorry. Stopped at /usr/local/bin/siemenstoafni line 857.
Any help would be much appreciated.
What is your actual command? There’s actually no command for siemenstoafni in the distribution. You probably want to use Dimon or a program like dcm2nii (part of mricron).
The command is: siemenstoafni -prefix XXX - rotobrick anat+orig ./DICOM
I have also tried
toler function, but I get the same error.
siemenstoafni -toler .2 -prefix run1 -rotobrick anat+orig ./DICOM
I`ll look into Dimon.
siemenstoafni is Fred Tam’s program. The last I had heard of it was almost 10 years ago, so I can’t offer too much advice here other than to contact him (fred.tam @ sri.utoronto.ca ). Dimon, to3d (both in AFNI), dcm2niix (provided by Chris Rorden) and mri_convert (by Doug Greve with the FreeSurfer package) are all good alternatives.