AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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dowdlelt
August 30, 2019 02:47PM
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 

-blur_sigma
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
    iopts.set_blurSigma(argv)
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!
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Subject Author Posted

epi_b0_correction doesn't allow blur sigma change

dowdlelt August 30, 2019 02:47PM

Re: epi_b0_correction doesn't allow blur sigma change

ptaylor August 30, 2019 05:15PM

Re: epi_b0_correction doesn't allow blur sigma change

dowdlelt August 30, 2019 06:27PM