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

Analysis carried out: 2024-05-01_16-23-58
Output directory: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3
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/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched_background_subtracted3', '/h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3', '-v', '4.57', '1.348', '1.348', '--orientation', 'sal', '--atlas', 'allen_mouse_10um']

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

Namespace:
image_paths: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched_background_subtracted3
brainreg_directory: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3
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: ['4.57', '1.348', '1.348']
orientation: sal
n_free_cpus: 4
debug: False
save_original_orientation: False
brain_geometry: full
sort_input_file: False
preprocessing: default


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

2024-05-01 16:23:58 PM - INFO - MainProcess fancylog.py:321 - Starting logging
2024-05-01 16:23:58 PM - INFO - MainProcess fancylog.py:322 - Not logging multiple processes
2024-05-01 16:23:58 PM - INFO - MainProcess cli.py:232 - Starting registration
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2024-05-01 16:23:59 PM - INFO - MainProcess main.py:52 - Loading raw image data
2024-05-01 16:23:59 PM - DEBUG - MainProcess load.py:65 - Data type is: directory of files
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2024-05-01 16:23:59 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2024-05-01 16:43:56 PM - INFO - MainProcess run.py:87 - Registering
2024-05-01 16:43:56 PM - INFO - MainProcess run.py:105 - Starting affine registration
2024-05-01 17:02:18 PM - INFO - MainProcess run.py:108 - Starting freeform registration
2024-05-01 17:03:25 PM - INFO - MainProcess run.py:111 - Starting segmentation
2024-05-01 17:04:21 PM - INFO - MainProcess run.py:114 - Segmenting hemispheres
2024-05-01 17:04:38 PM - INFO - MainProcess run.py:117 - Generating inverse (sample to atlas) transforms
2024-05-01 17:04:38 PM - DEBUG - MainProcess registration.py:130 - Generating inverse affine transform
2024-05-01 17:04:38 PM - DEBUG - MainProcess registration.py:169 - Registering sample to atlas
2024-05-01 17:06:47 PM - INFO - MainProcess run.py:120 - Transforming image to standard space
2024-05-01 17:07:25 PM - INFO - MainProcess run.py:126 - Generating deformation field
2024-05-01 17:07:25 PM - INFO - MainProcess registration.py:277 - Generating deformation field
2024-05-01 17:07:59 PM - INFO - MainProcess run.py:129 - Exporting images as tiff
2024-05-01 17:07:59 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-05-01 17:07:59 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-05-01 17:08:26 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-05-01 17:08:26 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-05-01 17:08:33 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-05-01 17:08:33 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-05-01 17:09:41 PM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-05-01 17:09:41 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-05-01 17:11:13 PM - INFO - MainProcess run.py:241 - Deleting intermediate niftyreg files
2024-05-01 17:11:13 PM - INFO - MainProcess main.py:92 - Calculating volumes of each brain area
2024-05-01 17:11:13 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-05-01 17:11:13 PM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3/registered_atlas.tiff
2024-05-01 17:11:24 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-05-01 17:11:24 PM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3/registered_hemispheres.tiff
2024-05-01 17:11:30 PM - WARNING - MainProcess volume.py:91 - Atlas value: 545 not found in registered atlas. Setting registered volume to 0.
2024-05-01 17:11:30 PM - INFO - MainProcess main.py:104 - Generating boundary image
2024-05-01 17:11:30 PM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-05-01 17:11:30 PM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3/registered_atlas.tiff
2024-05-01 17:11:49 PM - DEBUG - MainProcess boundaries.py:21 - Saving segmentation boundary image
2024-05-01 17:11:51 PM - INFO - MainProcess main.py:107 - brainreg completed. Results can be found here: /h20/Public/cebra/02CL89/analysis/brain_stack8_job_00836.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched_background_subtracted3
2024-05-01 17:11:51 PM - INFO - MainProcess cli.py:251 - Finished. Total time taken: 0:47:53.436482