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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ikbeneeneric
March 22, 2021 09:47AM
Hi there,

Thanks for your response.

The command we're running is:

align_epi_anat.py -anat2epi -anat " + functional_dir + " -save_skullstrip -suffix "
"al_junk -epi " + input_name_coregistration + " -epi_base 0 -epi_strip 3dAutomask -giant_move -volreg off -tshift off"

Where the functional_dir is a .nii.gz with more than one volume and the input_name_coregistration is a anatomical.nii.gz with only 1 volume.

This is in Python with string concatenation, the input files are saved in a variable because we're running it in a pipeline.

I am using Afni version AFNI_21.0.12 'Titus' on MacOS Big Sur.

Thanks,
Eric
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Subject Author Posted

align_epi_anat.py output 4D

ikbeneeneric March 22, 2021 08:48AM

Re: align_epi_anat.py output 4D

ptaylor March 22, 2021 09:23AM

Re: align_epi_anat.py output 4D

ikbeneeneric March 22, 2021 09:47AM

Re: align_epi_anat.py output 4D

ptaylor March 22, 2021 10:07AM

Re: align_epi_anat.py output 4D

ikbeneeneric March 22, 2021 10:24AM

Re: align_epi_anat.py output 4D

Daniel Glen March 22, 2021 12:35PM

Re: align_epi_anat.py output 4D

ikbeneeneric March 25, 2021 03:32AM

Re: align_epi_anat.py output 4D

ikbeneeneric March 25, 2021 05:45AM