Hi All,
I have created a fod_input and mask_input directory as recommended in the tutorial to then run population_template.
I get the following error;
File “/midas-data/software/mrtrix3_12.6.18/mrtrix3/bin/population_template”, line 442, in
run.command(‘mraverageheader -fill ’ + ’ ‘.join(input_filenames) + ’ - | mrresize - -voxel ‘+’,’.join(voxel_size)+’ average_header.mif’)
File “/midas-data/software/mrtrix3_12.6.18/mrtrix3/lib/mrtrix3/run.py”, line 197, in command
stderr_text = tempfiles[index][1].read().decode(‘utf-8’, errors=‘replace’)
TypeError: decode() takes no keyword arguments
I can’t figure out what this means or how to solve it. Any advice? (full text bellow) - Many thanks! Paul
population_template …/template/fod_input -mask_dir …/template/mask_input …/template/wmfod_template.mif -voxel_size 1.3
population_template: Generating a population-average template from 40 input images
population_template: SH series detected, performing FOD registration
population_template: initial alignment of images: mass
population_template: linear registration stages:
population_template: (00) rigid scale: 0.3000, niter: 100, lmax: 2
population_template: (01) rigid scale: 0.4000, niter: 100, lmax: 2
population_template: (02) rigid scale: 0.6000, niter: 100, lmax: 2
population_template: (03) rigid scale: 0.8000, niter: 100, lmax: 4
population_template: (04) rigid scale: 1.0000, niter: 100, lmax: 4
population_template: (05) rigid scale: 1.0000, niter: 100, lmax: 4
population_template: (06) affine scale: 0.3000, niter: 500, lmax: 2
population_template: (07) affine scale: 0.4000, niter: 500, lmax: 2
population_template: (08) affine scale: 0.6000, niter: 500, lmax: 2
population_template: (09) affine scale: 0.8000, niter: 500, lmax: 4
population_template: (10) affine scale: 1.0000, niter: 500, lmax: 4
population_template: (11) affine scale: 1.0000, niter: 500, lmax: 4
population_template: nonlinear registration stages:
population_template: (00) nonlinear scale: 0.3000, niter: 5, lmax: 2
population_template: (01) nonlinear scale: 0.4000, niter: 5, lmax: 2
population_template: (02) nonlinear scale: 0.5000, niter: 5, lmax: 2
population_template: (03) nonlinear scale: 0.6000, niter: 5, lmax: 2
population_template: (04) nonlinear scale: 0.7000, niter: 5, lmax: 2
population_template: (05) nonlinear scale: 0.8000, niter: 5, lmax: 2
population_template: (06) nonlinear scale: 0.9000, niter: 5, lmax: 2
population_template: (07) nonlinear scale: 1.0000, niter: 5, lmax: 2
population_template: (08) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (09) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (10) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (11) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (12) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (13) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (14) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: (15) nonlinear scale: 1.0000, niter: 5, lmax: 4
population_template: Generated temporary directory: /media/toshiba/complete/outputs/2012/population_template-tmp-HQSEII/
population_template: Changing to temporary directory (/media/toshiba/complete/outputs/2012/population_template-tmp-HQSEII/)
population_template: Generating initial template
Command: mraverageheader -fill XXX - | mrresize - -voxel 1.3,1.3,1.3 average_header.mif
Traceback (most recent call last):
File “/midas-data/software/mrtrix3_12.6.18/mrtrix3/bin/population_template”, line 442, in
run.command(‘mraverageheader -fill ’ + ’ ‘.join(input_filenames) + ’ - | mrresize - -voxel ‘+’,’.join(voxel_size)+’ average_header.mif’)
File “/midas-data/software/mrtrix3_12.6.18/mrtrix3/lib/mrtrix3/run.py”, line 197, in command
stderr_text = tempfiles[index][1].read().decode(‘utf-8’, errors=‘replace’)
TypeError: decode() takes no keyword arguments