Error in slice timing correction for vertical scanner (non standard PE direction)

[fm0lla]

Hi everyone,

I apologize in advance if this is not the correct place for this question.

I am currently using the newly released INDI-PRIME dataset (http://fcon_1000.projects.nitrc.org/indi/PRIME/uwmadison.html) from the UW-Wisconsin Madison university and I wanted to use the c-pac pipeline for the processing.

As far as I understand, they acquire the data in a monkey scanner with the monkeys being in a vertical position. This messes up a bit the commonly shared notions of image orientations and it has implications in the pre-processing.

While using the 3dTshift command from afni, the number of slices is interpreted to be the one in the k direction, not matching the number of slices field in the functional image header. Is there a way to circumvent this issue by changing the nhp-macaque.yml config file?

Thanks a lot,

Francesko