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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casparms
November 23, 2015 02:26PM
Hi Rick,
thanks for the advice!

This is the output of afni -ver
Version AFNI_2011_12_21_1014
[[Precompiled binary linux_xorg7_64: Sep 30 2013]]

Following your input, I played around with the filenames a bit, and I don't get the error anymore:


anatomy=VMR.ss+orig
tlrc_anatomy=VMR.ss+tlrc
epi=EPI+tshift+moco+wrap+orig

align_epi_anat.py -epi $base_folder/$data_folder/EPI+tshift+moco+wrap+mask+orig -anat $base_folder/$anat_folder/$anatomy -epi_base 0 -epi2anat -anat_has_skull no -epi_strip None -volreg off -tshift off -edge -suffix _algn -overwrite -rat_align -verb 0 -tlrc_apar $base_folder/$anat_folder/$tlrc_anatomy

It seems that AFNI didn't like that I tried to use the normalized version of the tlrc-ed anatomy.

Unfortunately however, the alignment of the EPI to the tlrc anatomy is completly off.
I have also tried to use Align_centers first, and then supply the (inverse) of that matrix as -pre_matrix to align_epi_anat.py, but with no success.

Caspar
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Subject Author Posted

NameError: global name 'anat_tlrc' is not defined

casparms November 20, 2015 01:07PM

Re: NameError: global name 'anat_tlrc' is not defined

rick reynolds November 23, 2015 01:34PM

Re: NameError: global name 'anat_tlrc' is not defined

casparms November 23, 2015 02:26PM

Re: NameError: global name 'anat_tlrc' is not defined

rick reynolds November 23, 2015 09:33PM

Re: NameError: global name 'anat_tlrc' is not defined

casparms November 24, 2015 02:52PM