**************  BRAINREG LOG  **************

Analysis carried out: 2024-04-24_17-03-20
Output directory: /h20/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01251.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted_iterative2
Current directory: /h20/home/iana/bio/notebooks/scripts/cebra
Version: 0.4.0

**************  GIT INFO  **************

Gitpython is not installed. Cannot check if software is in a git repository

**************  COMMAND LINE ARGUMENTS  **************

Command: /h20/home/iana/anaconda3/envs/ap/bin/brainreg 
Input arguments: ['/h20/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01251.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched_background_subtracted_iterative2', '/h20/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01251.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted_iterative2', '-v', '5.33', '1.444', '1.444', '--orientation', 'spr', '--atlas', 'allen_mouse_10_um']

**************  VARIABLES  **************

Namespace:
image_paths: /h20/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01251.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched_background_subtracted_iterative2
brainreg_directory: /h20/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01251.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted_iterative2
additional_images: None
atlas: allen_mouse_10_um
backend: niftyreg
affine_n_steps: 6
affine_use_n_steps: 5
freeform_n_steps: 6
freeform_use_n_steps: 4
bending_energy_weight: 0.95
grid_spacing: -10
smoothing_sigma_reference: -1.0
smoothing_sigma_floating: -1.0
histogram_n_bins_floating: 128
histogram_n_bins_reference: 128
voxel_sizes: ['5.33', '1.444', '1.444']
orientation: spr
n_free_cpus: 4
debug: False
save_original_orientation: False
brain_geometry: full
sort_input_file: False
preprocessing: default


**************  LOGGING  **************

2024-04-24 17:03:20 PM - INFO - MainProcess fancylog.py:321 - Starting logging
2024-04-24 17:03:20 PM - INFO - MainProcess fancylog.py:322 - Not logging multiple processes
2024-04-24 17:03:20 PM - INFO - MainProcess cli.py:232 - Starting registration