Hi Angelika,

EDIT: Oh my, Paul has gotten me back... maybe this post is moot.

Different software has created NIFTI datasets with different intentions in the sform/qform_code fields, making a value of 2 there ambiguous. It is generally applied incorrectly even.

To be sure, what is the output of:

nifti_tool -infiles 1002002_V001_DMSRun1.nii -disp_hdr -field sform_code -field qform_code

If those fields are equal to 2 AND if the EPI has not been registered to anything (in which case they should not be 2), then set the AFNI_NIFTI_VIEW environment variable to orig. This can be done in your $HOME/.afnirc file, in your shell environment or just in the script, as you prefer. For example, edit your ~/.afnirc file to have a line like:

AFNI_NIFTI_VIEW = orig

Please let me know how that goes.

Thanks,

- rick



Edited 1 time(s). Last edit at 02/17/2023 02:49PM by rick reynolds.