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

Analysis carried out: 2022-08-31_20-17-37
Output directory: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0
Current directory: /home/iana/src/analysis_pipeline
Version: 0.3.1

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

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

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

Command: /home/iana/anaconda3/envs/napari-clean/bin/brainreg 
Input arguments: ['/CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/channel_0', '/CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0', '-v', '5.33', '1.444', '1.444', '--orientation', 'spr', '--atlas', 'allen_mouse_10um', '--save-original-orientation']

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

Namespace:
image_paths: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/channel_0
brainreg_directory: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0
downsample_images: None
atlas: allen_mouse_10um
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: True
sort_input_file: False


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

2022-08-31 20:17:37 PM - INFO - MainProcess fancylog.py:307 - Starting logging
2022-08-31 20:17:37 PM - INFO - MainProcess fancylog.py:308 - Not logging multiple processes
2022-08-31 20:17:37 PM - INFO - MainProcess cli.py:205 - Starting registration
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 28
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 28
2022-08-31 20:17:39 PM - INFO - MainProcess main.py:49 - Loading raw image data
2022-08-31 20:17:39 PM - DEBUG - MainProcess load.py:66 - Data type is: directory of files
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 28
2022-08-31 20:17:39 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 28
2022-08-31 20:34:27 PM - INFO - MainProcess run.py:61 - Registering
2022-08-31 20:34:27 PM - INFO - MainProcess run.py:81 - Starting affine registration
2022-08-31 21:06:34 PM - INFO - MainProcess run.py:84 - Starting freeform registration
2022-08-31 21:07:32 PM - INFO - MainProcess run.py:87 - Starting segmentation
2022-08-31 21:07:45 PM - INFO - MainProcess run.py:90 - Segmenting hemispheres
2022-08-31 21:07:52 PM - INFO - MainProcess run.py:93 - Generating inverse (sample to atlas) transforms
2022-08-31 21:07:52 PM - DEBUG - MainProcess registration.py:139 - Generating inverse affine transform
2022-08-31 21:07:53 PM - DEBUG - MainProcess registration.py:178 - Registering sample to atlas
2022-08-31 21:10:40 PM - INFO - MainProcess run.py:96 - Transforming image to standard space
2022-08-31 21:11:04 PM - INFO - MainProcess run.py:102 - Generating deformation field
2022-08-31 21:11:04 PM - INFO - MainProcess registration.py:287 - Generating deformation field
2022-08-31 21:11:12 PM - INFO - MainProcess run.py:105 - Exporting images as tiff
2022-08-31 21:11:12 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI
2022-08-31 21:11:12 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2022-08-31 21:11:19 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI
2022-08-31 21:11:19 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2022-08-31 21:11:24 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI
2022-08-31 21:11:24 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2022-08-31 21:11:27 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI
2022-08-31 21:11:27 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2022-08-31 21:12:13 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI
2022-08-31 21:12:13 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2022-08-31 21:12:35 PM - INFO - MainProcess run.py:213 - Deleting intermediate niftyreg files
2022-08-31 21:12:36 PM - INFO - MainProcess main.py:83 - Calculating volumes of each brain area
2022-08-31 21:12:36 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack
2022-08-31 21:12:36 PM - DEBUG - MainProcess load.py:149 - Loading: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0/registered_atlas.tiff
2022-08-31 21:12:37 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack
2022-08-31 21:12:37 PM - DEBUG - MainProcess load.py:149 - Loading: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0/registered_hemispheres.tiff
2022-08-31 21:12:42 PM - WARNING - MainProcess volume.py:87 - Atlas value: 281 not found in registered atlas. Setting registered volume to 0.
2022-08-31 21:12:43 PM - WARNING - MainProcess volume.py:87 - Atlas value: 805 not found in registered atlas. Setting registered volume to 0.
2022-08-31 21:12:43 PM - INFO - MainProcess main.py:94 - Generating boundary image
2022-08-31 21:12:43 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack
2022-08-31 21:12:43 PM - DEBUG - MainProcess load.py:149 - Loading: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0/registered_atlas.tiff
2022-08-31 21:12:53 PM - DEBUG - MainProcess boundaries.py:22 - Saving segmentation boundary image
2022-08-31 21:12:53 PM - INFO - MainProcess main.py:100 - brainreg completed. Results can be found here: /CBI_Hive/Acquire/CEBRA/03CL12/analysis/composites_RSCM_v0.1_job_01116.ims/resolution_level_x/registration_channel_0
2022-08-31 21:12:54 PM - INFO - MainProcess cli.py:222 - Finished. Total time taken: 0:55:17.408753