epi_b0_correct monkey data

AFNI Message Board
1

Hi everyone,
I have a question: I have fmri data. I am using the tutorial in the in macaque demo and works perfect. I have this kind of data.
T1w - fieldmapAP - fieldmapPA - fmriAP(15min)- fmriPA(15 min)
The first part T1w aligment to the NMT2 no problem (@animal_warper)
However, I am not clear how to use epi_b0_correct, because in the demo afni_proc.py, uses only one epi, but it is the original epi and afni_proc does the alignment with T1w_warp2std, but if I use first epi_b0_correct I have provided the mask then it means I have to align the epi to the anat before, but then the output now it is align goes in the afni_proc.py, how should I proceed?
Thanks for any help

2

Thanks for the help

3

I am not completely sure, but I believe you should use the -blip_forward_dset and -blip_reverse_dset options using your fmriAP and fmriPA datasets in addition to those options for spatial warping to the macaque template described in the MACAQUE_DEMO scripts. For the fieldmap distortion correction instead, you could use epi_b0_correct.py as a separate procedure.

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In the beginning I was confused was the best method to apply and I had different comments and any of them was really clear. I have to say this is my first fmri data I am analyzing, I checked the boot-camps and reading I am convinced that both are reliable. Now I am using MACAQUE_DEMO_REST as guideline. Sorry if my question was not clear and very basic.
Thanks
Fabian