AttributeError: 'Nifti1Image' object has no attribute 'get_affine'

Melissa1909 commented 1 year ago

Dear MCRIBS developers, thank you for providing this great tool!

I am using MCRIBReconAll inside a docker container on a Linux machine (Ubuntu 18.04.6 LTS) as it has no Internet connection. When running

export MCRIBS_HOME=/MCRIBS
source ${MCRIBS_HOME}/SetUpMCRIBS.sh
export ANTSPATH=/sw/ants/2.3.5/bin
export PATH=${ANTSPATH}:${PATH}
SUBJECTS_DIR=/data_august/melissa/preterm_heterogeneity/dHCP
cd $SUBJECTS_DIR

MCRIBReconAll --all sub001

inside the container, I get the error: AttributeError: 'Nifti1Image' object has no attribute 'get_affine' See the full terminal messages attached in the log file. Any suggestions what the problem could be? Best, Melissa

MCRIBS_parcellation_020223.log

Dockerfile.txt

Melissa1909 commented 1 year ago

Hey, let me know if I can specify the problem. I have used other niftis but the error keeps occurring... Cheers, Melissa

chrisadamsonmcri commented 4 months ago

This is a deprecation in nibabel. I have fixed this locally. To fix it in your version, just search and replace .get_affine() with .affine in the python files. Apologies for the LONG delay.

DevelopmentalImagingMCRI / MCRIBS

AttributeError: 'Nifti1Image' object has no attribute 'get_affine' #9