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

Analysis carried out: 2024-04-25_09-50-51
Output directory: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2
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_stack7_job_00835.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched2', '/h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2', '-v', '4.57', '1.348', '1.348', '--orientation', 'sal', '--atlas', 'allen_mouse_10um']

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

Namespace:
image_paths: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/channel_1_notch_filtered_contrast_stretched2
brainreg_directory: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2
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  **************

2024-04-25 09:50:51 AM - INFO - MainProcess fancylog.py:321 - Starting logging
2024-04-25 09:50:51 AM - INFO - MainProcess fancylog.py:322 - Not logging multiple processes
2024-04-25 09:50:51 AM - INFO - MainProcess cli.py:232 - Starting registration
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2024-04-25 09:50:52 AM - INFO - MainProcess main.py:52 - Loading raw image data
2024-04-25 09:50:52 AM - DEBUG - MainProcess load.py:65 - Data type is: directory of files
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 32
2024-04-25 09:50:52 AM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 32
2024-04-25 10:11:32 AM - INFO - MainProcess run.py:87 - Registering
2024-04-25 10:11:32 AM - INFO - MainProcess run.py:105 - Starting affine registration
2024-04-25 10:33:00 AM - INFO - MainProcess run.py:108 - Starting freeform registration
2024-04-25 10:34:05 AM - INFO - MainProcess run.py:111 - Starting segmentation
2024-04-25 10:35:01 AM - INFO - MainProcess run.py:114 - Segmenting hemispheres
2024-04-25 10:35:18 AM - INFO - MainProcess run.py:117 - Generating inverse (sample to atlas) transforms
2024-04-25 10:35:18 AM - DEBUG - MainProcess registration.py:130 - Generating inverse affine transform
2024-04-25 10:35:18 AM - DEBUG - MainProcess registration.py:169 - Registering sample to atlas
2024-04-25 10:37:24 AM - INFO - MainProcess run.py:120 - Transforming image to standard space
2024-04-25 10:38:02 AM - INFO - MainProcess run.py:126 - Generating deformation field
2024-04-25 10:38:02 AM - INFO - MainProcess registration.py:277 - Generating deformation field
2024-04-25 10:38:41 AM - INFO - MainProcess run.py:129 - Exporting images as tiff
2024-04-25 10:38:41 AM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-04-25 10:38:41 AM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-04-25 10:39:10 AM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-04-25 10:39:10 AM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-04-25 10:39:18 AM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-04-25 10:39:18 AM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-04-25 10:40:35 AM - DEBUG - MainProcess load.py:101 - Data type is: NifTI
2024-04-25 10:40:35 AM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-04-25 10:42:15 AM - INFO - MainProcess run.py:241 - Deleting intermediate niftyreg files
2024-04-25 10:42:16 AM - INFO - MainProcess main.py:92 - Calculating volumes of each brain area
2024-04-25 10:42:16 AM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-04-25 10:42:16 AM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2/registered_atlas.tiff
2024-04-25 10:42:27 AM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-04-25 10:42:27 AM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2/registered_hemispheres.tiff
2024-04-25 10:42:35 AM - WARNING - MainProcess volume.py:91 - Atlas value: 1051 not found in registered atlas. Setting registered volume to 0.
2024-04-25 10:42:35 AM - INFO - MainProcess main.py:104 - Generating boundary image
2024-04-25 10:42:35 AM - DEBUG - MainProcess load.py:89 - Data type is: tif stack
2024-04-25 10:42:35 AM - DEBUG - MainProcess load.py:148 - Loading: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2/registered_atlas.tiff
2024-04-25 10:42:55 AM - DEBUG - MainProcess boundaries.py:21 - Saving segmentation boundary image
2024-04-25 10:42:58 AM - INFO - MainProcess main.py:107 - brainreg completed. Results can be found here: /h20/Public/cebra/02CL89/analysis/brain_stack7_job_00835.ims/resolution_level_x/registration_channel_1_notch_filtered_contrast_stretched2
2024-04-25 10:42:58 AM - INFO - MainProcess cli.py:251 - Finished. Total time taken: 0:52:07.125033