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

Analysis carried out: 2023-08-04_21-38-52
Output directory: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1
Current directory: /home/iana/bio/peace_pipe_line
Version: 0.4.0

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

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

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

Command: /home/iana/anaconda3/envs/ap/bin/brainreg 
Input arguments: ['/CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/channel_1', '/CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1', '-v', '5.33', '1.444', '1.444', '--orientation', 'spr', '--atlas', 'allen_mouse_10um', '--save-original-orientation']

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

Namespace:
image_paths: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/channel_1
brainreg_directory: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1
additional_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
brain_geometry: full
sort_input_file: False
preprocessing: default


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

2023-08-04 21:38:52 PM - INFO - MainProcess fancylog.py:321 - Starting logging
2023-08-04 21:38:52 PM - INFO - MainProcess fancylog.py:322 - Not logging multiple processes
2023-08-04 21:38:52 PM - INFO - MainProcess cli.py:232 - Starting registration
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2023-08-04 21:38:53 PM - INFO - MainProcess main.py:52 - Loading raw image data
2023-08-04 21:38:53 PM - DEBUG - MainProcess load.py:65 - Data type is: directory of files
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2023-08-04 21:38:53 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2023-08-04 21:56:20 PM - INFO - MainProcess run.py:87 - Registering
2023-08-04 21:56:20 PM - INFO - MainProcess run.py:105 - Starting affine registration
2023-08-04 22:16:58 PM - INFO - MainProcess run.py:108 - Starting freeform registration
2023-08-04 22:18:06 PM - INFO - MainProcess run.py:111 - Starting segmentation
2023-08-04 22:19:03 PM - INFO - MainProcess run.py:114 - Segmenting hemispheres
2023-08-04 22:19:19 PM - INFO - MainProcess run.py:117 - Generating inverse (sample to atlas) transforms
2023-08-04 22:19:19 PM - DEBUG - MainProcess registration.py:130 - Generating inverse affine transform
2023-08-04 22:19:19 PM - DEBUG - MainProcess registration.py:169 - Registering sample to atlas
2023-08-04 22:21:20 PM - INFO - MainProcess run.py:120 - Transforming image to standard space
2023-08-04 22:21:57 PM - INFO - MainProcess run.py:126 - Generating deformation field
2023-08-04 22:21:57 PM - INFO - MainProcess registration.py:277 - Generating deformation field
2023-08-04 22:22:34 PM - INFO - MainProcess run.py:129 - Exporting images as tiff
2023-08-04 22:22:34 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2023-08-04 22:22:34 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2023-08-04 22:24:58 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2023-08-04 22:24:59 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2023-08-04 22:27:39 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2023-08-04 22:27:39 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2023-08-04 22:28:18 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2023-08-04 22:28:18 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2023-08-04 22:32:20 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2023-08-04 22:32:20 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2023-08-04 22:39:41 PM - INFO - MainProcess run.py:241 - Deleting intermediate niftyreg files
2023-08-04 22:39:42 PM - INFO - MainProcess main.py:92 - Calculating volumes of each brain area
2023-08-04 22:39:42 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2023-08-04 22:39:42 PM - DEBUG - MainProcess load.py:148 - Loading: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1/registered_atlas.tiff
2023-08-04 22:39:55 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2023-08-04 22:39:55 PM - DEBUG - MainProcess load.py:148 - Loading: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1/registered_hemispheres.tiff
2023-08-04 22:40:03 PM - INFO - MainProcess main.py:104 - Generating boundary image
2023-08-04 22:40:03 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2023-08-04 22:40:03 PM - DEBUG - MainProcess load.py:148 - Loading: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1/registered_atlas.tiff
2023-08-04 22:40:24 PM - DEBUG - MainProcess boundaries.py:21 - Saving segmentation boundary image
2023-08-04 22:40:26 PM - INFO - MainProcess main.py:107 - brainreg completed. Results can be found here: /CBI_Hive/Public/cebra/03CL47/analysis/composites_RSCM_v0.1_job_01253.ims/resolution_level_x/registration_channel_1
2023-08-04 22:40:27 PM - INFO - MainProcess cli.py:251 - Finished. Total time taken: 1:01:34.545993