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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Jeff Phillips
January 05, 2009 06:03PM
Hello all,

I have run into a stubborn error with align_epi_anat.py, and I could use your help making sense of it. My command line is:

$ align_epi_anat.py -anat mprage.bet.nii.gz -epi run1.nii.gz -epi_base 5 -anat_has_skull no -volreg off -tshift off -big_move

The result of this command is below. By the way, I thought that the problem could be with the input image format, but I got a similar error using .BRIK files as inputs.

#++ align_epi_anat version: 1.04
#++ turning off volume registration
#Script is running:
3dAttribute DELTA /home/jeffreyp/fMRI_training/s1/run1.nii.gz
#++ Spacing for EPI to tlrc alignment is -3.800000
#++ Removing all the temporary files
#Script is running:
rm -f __tt_run1*
#Script is running:
rm -f __tt_mprage.bet*
#Script is running:
3dcopy /home/jeffreyp/fMRI_training/s1/mprage.bet.nii.gz __tt_mprage.bet+orig
Error: Second index j=1 is >= to number of elements (1) in 0th line of output

The temp files left behind are...

__tt_mprage.bet+orig.BRIK
__tt_mprage.bet+orig.HEAD

...and no other output exists. If you can steer me in the right direction, I would appreciate it. Thanks,

Jeff
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Subject Author Posted

align_epi_anat error

Jeff Phillips January 05, 2009 06:03PM

Re: align_epi_anat error

Daniel Glen January 06, 2009 10:22AM