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

Ran at : 2024-08-26_12-29-21
Output directory: ./aligned_PU_atlas
Current directory: /mnt/cup/PNI-centers/LightSheetData/lightserv/jk8386/kaminsky_01-jj124
Version: 1.0.10

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

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

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

Command: /usr/people/kalmbach/.conda/envs/iblenv/bin/brainreg 
Input arguments: ['./ch00', './aligned_PU_atlas', '-v', '10', '5.91', '5.91', '--orientation', 'sal', '--atlas', 'princeton_mouse_20um', '--additional', './ch01']

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

Namespace:
image_paths: ./ch00
brainreg_directory: ./aligned_PU_atlas
additional_images: ['./ch01']
atlas: princeton_mouse_20um
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: ['10', '5.91', '5.91']
orientation: sal
n_free_cpus: 2
debug: False
save_original_orientation: False
brain_geometry: full
sort_input_file: False
preprocessing: default


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

2024-08-26 12:29:21 PM - INFO - MainProcess fancylog.py:326 - Starting logging
2024-08-26 12:29:21 PM - INFO - MainProcess fancylog.py:327 - Not logging multiple processes
2024-08-26 12:29:21 PM - INFO - MainProcess cli.py:286 - Starting registration
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:231 - Determining the maximum number of CPU cores to use
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:236 - Number of CPU cores available is: 42
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:263 - Setting number of processes to: 42
2024-08-26 12:29:22 PM - INFO - MainProcess main.py:48 - Loading raw image data
2024-08-26 12:29:22 PM - DEBUG - MainProcess load.py:106 - Data type is: directory of files
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:231 - Determining the maximum number of CPU cores to use
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:236 - Number of CPU cores available is: 42
2024-08-26 12:29:22 PM - DEBUG - MainProcess system.py:263 - Setting number of processes to: 42
2024-08-26 12:30:35 PM - INFO - MainProcess run.py:86 - Registering
2024-08-26 12:30:35 PM - INFO - MainProcess run.py:104 - Starting affine registration
2024-08-26 12:33:50 PM - INFO - MainProcess run.py:107 - Starting freeform registration
2024-08-26 12:34:00 PM - INFO - MainProcess run.py:110 - Starting segmentation
2024-08-26 12:34:05 PM - INFO - MainProcess run.py:113 - Segmenting hemispheres
2024-08-26 12:34:07 PM - INFO - MainProcess run.py:116 - Generating inverse (sample to atlas) transforms
2024-08-26 12:34:07 PM - DEBUG - MainProcess registration.py:133 - Generating inverse affine transform
2024-08-26 12:34:07 PM - DEBUG - MainProcess registration.py:172 - Registering sample to atlas
2024-08-26 12:34:15 PM - INFO - MainProcess run.py:119 - Transforming image to standard space
2024-08-26 12:34:18 PM - INFO - MainProcess run.py:125 - Generating deformation field
2024-08-26 12:34:18 PM - INFO - MainProcess registration.py:280 - Generating deformation field
2024-08-26 12:34:22 PM - INFO - MainProcess run.py:128 - Exporting images as tiff
2024-08-26 12:34:22 PM - DEBUG - MainProcess load.py:139 - Data type is: NifTI
2024-08-26 12:34:23 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-08-26 12:34:26 PM - DEBUG - MainProcess load.py:139 - Data type is: NifTI
2024-08-26 12:34:26 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-08-26 12:34:28 PM - DEBUG - MainProcess load.py:139 - Data type is: NifTI
2024-08-26 12:34:28 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-08-26 12:34:31 PM - DEBUG - MainProcess load.py:139 - Data type is: NifTI
2024-08-26 12:34:31 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-08-26 12:34:43 PM - INFO - MainProcess run.py:176 - Saving additional downsampled images
2024-08-26 12:34:43 PM - INFO - MainProcess run.py:178 - Processing: ch01
2024-08-26 12:34:43 PM - DEBUG - MainProcess load.py:106 - Data type is: directory of files
2024-08-26 12:34:43 PM - DEBUG - MainProcess system.py:231 - Determining the maximum number of CPU cores to use
2024-08-26 12:34:43 PM - DEBUG - MainProcess system.py:236 - Number of CPU cores available is: 42
2024-08-26 12:34:43 PM - DEBUG - MainProcess system.py:263 - Setting number of processes to: 42
2024-08-26 12:35:09 PM - INFO - MainProcess run.py:223 - Transforming to standard space
2024-08-26 12:35:11 PM - DEBUG - MainProcess load.py:139 - Data type is: NifTI
2024-08-26 12:35:11 PM - INFO - MainProcess batteryrunners.py:268 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
2024-08-26 12:35:15 PM - INFO - MainProcess run.py:238 - Deleting intermediate niftyreg files
2024-08-26 12:35:16 PM - INFO - MainProcess main.py:85 - Calculating volumes of each brain area
2024-08-26 12:35:16 PM - DEBUG - MainProcess load.py:130 - Data type is: tif stack
2024-08-26 12:35:16 PM - DEBUG - MainProcess load.py:193 - Loading: aligned_PU_atlas/registered_atlas.tiff
2024-08-26 12:35:17 PM - DEBUG - MainProcess load.py:130 - Data type is: tif stack
2024-08-26 12:35:17 PM - DEBUG - MainProcess load.py:193 - Loading: aligned_PU_atlas/registered_hemispheres.tiff
2024-08-26 12:35:22 PM - WARNING - MainProcess volume.py:90 - Atlas value: 30 not found in registered atlas. Setting registered volume to 0.
2024-08-26 12:35:22 PM - WARNING - MainProcess volume.py:90 - Atlas value: 118 not found in registered atlas. Setting registered volume to 0.
2024-08-26 12:35:23 PM - WARNING - MainProcess volume.py:90 - Atlas value: 975 not found in registered atlas. Setting registered volume to 0.
2024-08-26 12:35:23 PM - INFO - MainProcess main.py:97 - Generating boundary image
2024-08-26 12:35:23 PM - DEBUG - MainProcess load.py:130 - Data type is: tif stack
2024-08-26 12:35:23 PM - DEBUG - MainProcess load.py:193 - Loading: aligned_PU_atlas/registered_atlas.tiff
2024-08-26 12:35:28 PM - DEBUG - MainProcess boundaries.py:22 - Saving segmentation boundary image
2024-08-26 12:35:29 PM - INFO - MainProcess main.py:100 - brainreg completed. Results can be found here: ./aligned_PU_atlas
2024-08-26 12:35:29 PM - INFO - MainProcess cli.py:305 - Finished. Total time taken: 0:06:08.460759