epi_b0_correction doesn't allow blur sigma change

Attempting to use epi_b0_correct.py and it looks like it works well, however, I am unable to change the blurring parameter using the


command, as in:

epi_b0_correct.py -prefix corrected3 -in_freq phase_int2.nii.gz -in_epi cmrr_mbep2d_bold_84slices_1pt8mm_1600TR_MB3_R2.nii.gz -in_magn gre_field_mappingb_42slices_3pt6mm_e1.nii.gz -blur_sigma 6 -in_epi_json cmrr_mbep2d_bold_84slices_1pt8mm_1600TR_MB3_R2.json -epi_pe_dir AP -scale_freq 0.311785 

Attempting this results in the following error

Traceback (most recent call last):
  File "/Users/logan/abin/epi_b0_correct.py", line 74, in <module>
    iopts = lb0.parse_args_b0_corr(sys.argv)
  File "/Users/logan/abin/lib_b0_corr.py", line 1602, in parse_args_b0_corr
AttributeError: 'iopts_b0_corr' object has no attribute 'set_blurSigma'

I updated afni this morning, reporting

Precompiled binary macos_10.12_local: Aug 29 2019 (Version AFNI_19.2.21 'Claudius')

Everything works if I try not to set that parameter - thanks for working on this fieldmap approach!

Hi, Logan–

Thanks for testing it out; I have squashed that bug now, and pushed the new version to the git repo. It will be in the next build (which will probably be soon/this weekend); if you want to pre-empt that, you can grab “lib_b0_corr.py” from the repo, and you should be aaaalll set. As a bonus, the blur sigma is now also output in the *pars.txt file.

Also, all credit for this B0 correction work goes to Vinai “The Corrector” Roopchansingh; merely translating his work on this.


Fantastic, thanks for the quick fix. I say credit to originators and translators! I’ll see if I can keep breaking, i mean beta testing it