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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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ptaylor
March 09, 2023 07:37AM
Thanks for that full output.

I am now running this command with "-child_epi .." and "-tshift_opts ..", and still not getting an error: 
align_epi_anat.py         -verb 5                                            \
    -anat         FT_anat+orig.HEAD                                          \
    -epi          pb00.FT.r01.tcat+orig.HEAD                                 \
    -anat2epi                                                                \
    -giant_move                                                              \
    -cost         lpc+                                                       \
    -epi_base     mean                                                       \
    -child_epi    pb00.FT.r02.tcat+orig pb00.FT.r03.tcat+orig     \
    -tshift_opts  '-ignore 4'                                                \
    -output_dir   ./odir                                                     \
    -save_vr                                                                 \
    -suffix       _al                                                        \
    -overwrite \
    |& tee out_my_aea.txt

However, I think the different must be that you actually have slice shifts to apply to your data, and the EPIs that I have do not have those. I will ping you to get your datasets, if that is OK, to use those directly, but I suspect that is where the error is popping up; I think the 'mean' label is being misapplied there.

--pt
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Subject Author Posted

options for -epi_base on align_epi_anat.py

wgraves March 08, 2023 04:05PM

Re: options for -epi_base on align_epi_anat.py

ptaylor March 08, 2023 06:08PM

Re: options for -epi_base on align_epi_anat.py

wgraves March 08, 2023 09:24PM

Re: options for -epi_base on align_epi_anat.py

ptaylor March 09, 2023 07:37AM

Re: options for -epi_base on align_epi_anat.py

wgraves March 09, 2023 09:34AM