gift-surg / niftymic Goto Github PK

I have observed regularly that the reconstruction in subject space crashes unexpectedly.
Typically several warnings from fslorient appear and shortly after the program crashes during the first volume-to-volume registration (see below for an example of logs associated with the problem).

Monitoring the memory in some cases for which it happens, I think the program stops due to a Memory Error.

There is maybe not much that can be done to prevent the memory error except using a machine with more memory. However, NiftyMIC should state the memory error correctly. The current logs are inaccurate and confusing.

I will try to investigate how to catch this memory error.

Example of logs associated with this problem:
*** 12/12 -- UZL00181/Study1 ***
['t2_haste_body_sag_24.nii.gz', 't2_haste_brain_ax_9.nii.gz', 't2_haste_brain_cor_10.nii.gz', 't2_haste_brain_cor_12.nii.gz', 't2_haste_brain_cor_14.nii.gz', 't2_haste_brain_cor_16.nii.gz', 't2_haste_brain_cor_18.nii.gz', 't2_haste_brain_cor_19.nii.gz', 't2_haste_brain_sag_11.nii.gz', 't2_haste_uterus_2.nii.gz']
--- Searching for suitable target stack ... done
--- File written to '/home/lucasf/workspace/giftcloudsrr/src/target_stacks.json'.

---- Executed command: ----
niftymic_run_reconstruction_pipeline
--filenames /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_body_sag_24.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_ax_9.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_10.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_12.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_14.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_16.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_19.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_sag_11.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_uterus_2.nii.gz
--filenames-masks /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_body_sag_24.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_ax_9.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_10.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_12.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_14.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_16.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_18.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_19.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_sag_11.nii.gz /home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_uterus_2.nii.gz
--dir-output /home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr
--bias-field-correction 0
--target-stack /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz
--run-bias-field-correction 0
--run-recon-subject-space 1
--run-recon-template-space 0
--run-diagnostics 0
--verbose 1
--log-config 1
--threshold 0.800000

*** Configuration: ***
--- alpha: 0.01
--- automatic_target_stack: 1
--- bias_field_correction: 0
--- config: None
--- dir_output: /home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr
--- filenames:
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_body_sag_24.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_ax_9.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_10.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_12.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_14.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_16.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_19.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_sag_11.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_uterus_2.nii.gz
--- filenames_masks:
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_body_sag_24.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_ax_9.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_10.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_12.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_14.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_16.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_18.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_19.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_sag_11.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_uterus_2.nii.gz
--- initial_transform: None
--- intensity_correction: 1
--- interleave: 3
--- isotropic_resolution: None
--- iter_max: 10
--- log_config: 1
--- multiresolution: 0
--- outlier_rejection: 1
--- prefix_output: srr_
--- reference: None
--- reference_mask: None
--- run_bias_field_correction: 0
--- run_diagnostics: 0
--- run_recon_subject_space: 1
--- run_recon_template_space: 0
--- s2v_hierarchical: False
--- sda: False
--- search_angle: 180
--- slice_thicknesses: None
--- suffix_mask:
--- target_stack: /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz
--- template: None
--- template_mask: None
--- threshold: 0.8
--- threshold_first: 0.5
--- two_step_cycles: 3
--- v2v_robust: False
--- verbose: 1

NiftyMIC version: 0.7.4

--- File written to '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr/config_run_reconstruction_pipeline_20200107-092104.json'.

---- Executed command: ----
niftymic_reconstruct_volume
--filenames '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_body_sag_24.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_ax_9.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_10.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_12.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_14.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_16.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_19.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_sag_11.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_uterus_2.nii.gz'
--filenames-masks '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_body_sag_24.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_ax_9.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_10.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_12.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_14.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_16.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_18.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_19.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_sag_11.nii.gz' '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_uterus_2.nii.gz'
--multiresolution 0
--target-stack '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz'
--output '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr/recon_subject_space/srr_subject.nii.gz'
--suffix-mask ''
--intensity-correction 1
--alpha 0.01
--iter-max 10
--two-step-cycles 3
--outlier-rejection 1
--threshold-first 0.500000
--threshold 0.800000
--verbose 1
--log-config 1
--isotropic-resolution 0.800000

WARNING (theano.configdefaults): install mkl with conda install mkl-service: No module named 'mkl'
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

*** Configuration: ***
--- alpha: 0.01
--- alpha_first: 0.2
--- bias_field_correction: 0
--- boundary_stacks:
10
10
0
--- config: None
--- dilation_radius: 3
--- extra_frame_target: 10
--- filenames:
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_body_sag_24.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_ax_9.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_10.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_12.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_14.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_16.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_19.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_sag_11.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_uterus_2.nii.gz
--- filenames_masks:
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_body_sag_24.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_ax_9.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_10.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_12.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_14.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_16.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_18.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_cor_19.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_brain_sag_11.nii.gz
/home/lucasf/data/giftcloudsrr/UZL00181/Study1/seg/t2_haste_uterus_2.nii.gz
--- intensity_correction: 1
--- interleave: 3
--- isotropic_resolution: 0.8
--- iter_max: 10
--- iter_max_first: 5
--- iterations: 15
--- log_config: 1
--- metric: Correlation
--- metric_radius: 10
--- multiresolution: 0
--- outlier_rejection: 1
--- output: /home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr/recon_subject_space/srr_subject.nii.gz
--- reconstruction_type: TK1L2
--- reference: None
--- reference_mask: None
--- s2v_hierarchical: False
--- sda: False
--- search_angle: 45
--- shrink_factors:
3
2
1
--- sigma: 1
--- slice_thicknesses: None
--- smoothing_sigmas:
1.5
1
0
--- subfolder_motion_correction: motion_correction
--- suffix_mask:
--- target_stack: /home/lucasf/data/giftcloudsrr/UZL00181/Study1/nifti/t2_haste_brain_cor_18.nii.gz
--- threshold: 0.8
--- threshold_first: 0.5
--- transforms_history: 0
--- two_step_cycles: 3
--- use_masks_srr: 0
--- v2v_method: RegAladin
--- v2v_robust: False
--- verbose: 1
--- viewer: itksnap
--- write_motion_correction: 1

NiftyMIC version: 0.7.4

--- File written to '/home/lucasf/data/giftcloudsrr/UZL00181/Study1/srr/recon_subject_space/config_reconstruct_volume_20200107-092106.json'.

*** Read Data ***
--- 10 input stacks read for further processing

*** Data Preprocessing ***
--- 10 stacks were loaded for data preprocessing
--- Crop stacks to their masks

*** Volume-to-Volume Registration ***
--- Volume-to-Volume Registration -- Stack 1/10

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
--- WARNING: Only q-form is set as fslorient was not successful!
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
--- WARNING: Only q-form is set as fslorient was not successful!
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
--- WARNING: Only q-form is set as fslorient was not successful!
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
--- WARNING: Only q-form is set as fslorient was not successful!
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

200107-09:21:19,618 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
Traceback (most recent call last):
File "/home/lucasf/workspace/srr/bin/niftymic_reconstruct_volume", line 11, in
load_entry_point('NiftyMIC==0.7.4', 'console_scripts', 'niftymic_reconstruct_volume')()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/application/reconstruct_volume.py", line 260, in main
v2vreg.run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 65, in run
self._run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 171, in _run
self._registration_method.run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/registration/registration_method.py", line 169, in run
self._run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/registration/niftyreg.py", line 97, in _run
self._registration_method.run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/simplereg/simple_itk_registration_base.py", line 245, in run
self._run()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/simplereg/niftyreg.py", line 124, in _run
nreg = nipype.interfaces.niftyreg.RegAladin()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/nipype/interfaces/niftyreg/base.py", line 58, in init
_version = self.version_from_command()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 747, in version_from_command
stderr=sp.PIPE,
File "/home/lf18/anaconda3/lib/python3.7/subprocess.py", line 775, in init
restore_signals, start_new_session)
File "/home/lf18/anaconda3/lib/python3.7/subprocess.py", line 1453, in _execute_child
restore_signals, start_new_session, preexec_fn)
OSError: [Errno 12] Cannot allocate memory
Traceback (most recent call last):
File "/home/lucasf/workspace/srr/bin/niftymic_run_reconstruction_pipeline", line 11, in
load_entry_point('NiftyMIC==0.7.4', 'console_scripts', 'niftymic_run_reconstruction_pipeline')()
File "/home/lucasf/workspace/srr/lib/python3.7/site-packages/niftymic/application/run_reconstruction_pipeline.py", line 295, in main
raise RuntimeError("Reconstruction in subject space failed")
RuntimeError: Reconstruction in subject space failed

I am in the "Reconstruction Space Generation" step. While running reconstruction pipeline I received the following error. Would anyone be able to explain the error and how to resolve? I am using Python 3.10.

Code:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.10/bin/niftymic_reconstruct_volume", line 33, in
sys.exit(load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume')())
File "/NiftyMIC/niftymic/application/reconstruct_volume.py", line 314, in main
joint_image_mask_builder.run()
File "/NiftyMIC/niftymic/utilities/joint_image_mask_builder.py", line 52, in run
mask_sitk = thresholder.Execute(mask_sitk, 0, 0.5, 0, 1)
TypeError: BinaryThresholdImageFilter.Execute() takes 2 positional arguments but 6 were given
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.10/bin/niftymic_run_reconstruction_pipeline", line 33, in
sys.exit(load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_run_reconstruction_pipeline')())
File "/NiftyMIC/niftymic/application/run_reconstruction_pipeline.py", line 295, in main
raise RuntimeError("Reconstruction in subject space failed")
RuntimeError: Reconstruction in subject space failed

with the option --reconstruction-mask and a mask that masks out slices at the top of the stack, 'simulate_slice' is left uninitialized:

Traceback (most recent call last): File ".../NiftyMIC//niftymic/validation/simulate_stacks_from_reconstruction.py", line 168, in <module> main() File ".../NiftyMIC//niftymic/validation/simulate_stacks_from_reconstruction.py", line 126, in main simulated_slice.sitk_mask) UnboundLocalError: local variable 'simulated_slice' referenced before assignment
I added a try-catch block, but there's prob. a better way of fixing this.

Helo Trying to run niftymic_segment_fetal_brains // fetal_brain_seg.py but it gaves an error while it looks it is OK
I'm runnig in a apptainer//singularity container

see:

Apptainer> ls
CC2-1-Ax.nii
Apptainer> fetal_brain_seg.py --input_names CC2-1-Ax.nii --segment_output_names  seg/CC2-1-Ax.nii
*** Config file
/usr/local/lib/python3.6/site-packages/monaifbs/config/monai_dynUnet_inference_config.yml
*** Input data: 
CC2-1-Ax.nii
*** MONAI config: 
MONAI version: 0.3.0
Python version: 3.6.8 (default, Nov 16 2020, 16:55:22)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-44)]
OS version: Linux (4.18.0-240.22.1.el8_3.x86_64)
Numpy version: 1.19.5
Pytorch version: 1.10.2+cu102
MONAI flags: HAS_EXT = False, USE_COMPILED = False

Optional dependencies:
Pytorch Ignite version: 0.4.2
Nibabel version: 3.2.2
scikit-image version: 0.17.2
Pillow version: 8.4.0
Tensorboard version: 2.8.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: 4.13.0
tqdm version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

*** Network inference config: 
device:
  num_workers: 1
inference:
  batch_size_inference: 1
  inplane_size:
  - 448
  - 512
  model_to_load: /usr/local/lib/python3.6/site-packages/monaifbs/models/checkpoint_dynUnet_DiceXent.pt
  nr_out_channels: 2
  probability_threshold: 0.5
  spacing:
  - 0.8
  - 0.8
  - -1.0
output:
  out_dir: seg
  out_postfix: seg

Considering patch size = [448, 512, 1]
Using device: cpu
***  Preparing data ... 
***  Preparing network ... 
***  Preparing evaluator ... 
Using sigmoid=False and softmax=True as final activation
***  Running evaluator ... 
INFO:ignite.engine.engine.DynUNetEvaluator:Engine run resuming from iteration 0, epoch 0 until 1 epochs
INFO:ignite.engine.engine.DynUNetEvaluator:Restored all variables from /usr/local/lib/python3.6/site-packages/monaifbs/models/checkpoint_dynUnet_DiceXent.pt
INFO:ignite.engine.engine.DynUNetEvaluator:saved all the model outputs into files.
INFO:ignite.engine.engine.DynUNetEvaluator:Epoch[1] Complete. Time taken: 00:02:31
INFO:ignite.engine.engine.DynUNetEvaluator:Engine run complete. Time taken: 00:02:32
Done!
Traceback (most recent call last):
  File "/usr/local/bin/fetal_brain_seg.py", line 104, in <module>
    "check if the segmentation pipeline has failed".format(out_filename))
FileNotFoundError: Network output file seg/CC2-1-Ax/CC2-1-Ax_seg.nii not found, check if the segmentation pipeline has failed

BUT

Apptainer> ls seg/CC2-1-Ax/CC2-1-Ax_seg.nii*   
seg/CC2-1-Ax/CC2-1-Ax_seg.nii.gz

seems the detection of file has some flaws on fetal_brain_seg.py about out_filename detection.

regards

Eric

Hi, I'm running the installation_test.py after installing all dependencies. However, there reports an error which seems to be related to c3d and I don't know how to solve it.

python -m nose tests/installation_test.py
E..

ERROR: test_fsl (tests.installation_test.InstallationTest)

Traceback (most recent call last):
File "/home/mwj/NiftyMIC/tests/installation_test.py", line 41, in test_fsl
registration_method.run()
File "/home/mwj/NiftyMIC/niftymic/registration/registration_method.py", line 169, in run
self._run()
File "/home/mwj/NiftyMIC/niftymic/registration/flirt.py", line 101, in _run
self._registration_method.run()
File "/home/mwj/anaconda3/lib/python3.7/site-packages/simplereg/simple_itk_registration_base.py", line 245, in run
self._run()
File "/home/mwj/anaconda3/lib/python3.7/site-packages/simplereg/flirt.py", line 101, in _run
self._registration_transform_sitk = self._convert_to_sitk_transform()
File "/home/mwj/anaconda3/lib/python3.7/site-packages/simplereg/flirt.py", line 120, in _convert_to_sitk_transform
verbose=self._verbose,
File "/home/mwj/anaconda3/lib/python3.7/site-packages/simplereg/flirt_to_simpleitk_converter.py", line 54, in convert_flirt_to_sitk_transform
c3d.run()
File "/home/mwj/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/home/mwj/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 792, in _run_interface
self.raise_exception(runtime)
File "/home/mwj/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 723, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
c3d_affine_tool -ref /tmp/tmpc32c_pa9/FLIRT/fixed.nii.gz -src /tmp/tmpc32c_pa9/FLIRT/moving.nii.gz /tmp/tmpc32c_pa9/FLIRT/registration_transform.txt -fsl2ras -oitk /tmp/tmpc32c_pa9/FLIRT/registration_transform_sitk.txt
Standard output:

Standard error:
terminate called after throwing an instance of 'char const*'
Aborted (core dumped)
Return code: 134
...
...
...

Ran 3 tests in 18.550s

FAILED (errors=1)"

Dear all,

Thank you for this great package.
When I run the niftymic_reconstruct_volume, the program is always “Killed”.
I have set the memory to the maximum memory（16G + 4G swap）, but still not enough. When the memory usage of container reaches 16G, the program will be "killed". I wonder how can I solve this problem?

`# niftymic_reconstruct_volume
--filenames /www/cor/T2_bias.nii.gz /www/sag/T2_bias.nii.gz /www/tra/T2_bias.nii.gz
--filenames-masks /www/cor/T2_label.nii.gz /www/sag/T2_label.nii.gz /www/tra/T2_label.nii.gz
--output /www/srr.nii.gz \

*** Configuration: ***
--- alpha: 0.015
--- alpha_first: 0.2
--- bias_field_correction: 0
--- boundary_stacks:
10
10
0
--- config: None
--- dilation_radius: 3
--- extra_frame_target: 10
--- filenames:
/www/cor/T2_bias.nii.gz
/www/sag/T2_bias.nii.gz
/www/tra/T2_bias.nii.gz
--- filenames_masks:
/www/cor/T2_label.nii.gz
/www/sag/T2_label.nii.gz
/www/tra/T2_label.nii.gz
--- intensity_correction: 1
--- interleave: 3
--- isotropic_resolution: 1
--- iter_max: 10
--- iter_max_first: 5
--- iterations: 15
--- log_config: 1
--- metric: Correlation
--- metric_radius: 10
--- multiresolution: 0
--- outlier_rejection: 1
--- output: /www/srr.nii.gz
--- reconstruction_type: TK1L2
--- reference: None
--- reference_mask: None
--- s2v_hierarchical: False
--- sda: False
--- search_angle: 45
--- shrink_factors:
3
2
1
--- sigma: 1
--- slice_thicknesses: None
--- smoothing_sigmas:
1.5
1
0
--- subfolder_motion_correction: motion_correction
--- suffix_mask: _mask
--- target_stack: None
--- threshold: 0.8
--- threshold_first: 0.5
--- transforms_history: 0
--- two_step_cycles: 3
--- use_masks_srr: 0
--- v2v_method: RegAladin
--- v2v_robust: False
--- verbose: 0
--- viewer: itksnap
--- write_motion_correction: 1

NiftyMIC version: 0.9

--- File written to '/www/config_reconstruct_volume_20220604-094944.json'.

*** Read Data ***
--- 3 input stacks read for further processing

*** Data Preprocessing ***
--- 3 stacks were loaded for data preprocessing
--- Crop stacks to their masks

*** Volume-to-Volume Registration ***
--- Volume-to-Volume Registration -- Stack 1/3
220604-09:50:09,211 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
220604-09:50:09,343 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
--- Volume-to-Volume Registration -- Stack 2/3
220604-09:50:47,548 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
220604-09:50:47,655 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
--- Volume-to-Volume Registration -- Stack 3/3
220604-09:51:32,424 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0
220604-09:51:32,529 nipype.interface WARNING:
version_from_command member of CommandLine was Deprecated in nipype-1.0.0 and deleted in 1.1.0

*** Intensity Correction ***
--- Stack 1 (T2_bias): Reference image. Skipped.
--- Stack 2 (T2_bias): Intensity Correction ... done (c1 = 0.908708)
--- Stack 3 (T2_bias): Intensity Correction ... done (c1 = 0.949986)

*** Reconstruction Space Generation ***
--- Isotropic reconstruction space with 1 mm resolution is created
--- Isotropic reconstruction space is centered around joint stack masks.

*** First Estimate of HR Volume ***

*** SDA Approximation Image ***
--- Chosen SDA approach: Shepard-YVV
--- Smoothing parameter sigma = [1. 1. 1.]
--- Stack 1/3
--- Stack 2/3
--- Stack 3/3
--- Required computational time: 0:00:19.953441

*** SDA Approximation Image Mask ***
--- Chosen SDA approach: Shepard-YVV
--- Smoothing parameter sigma = [1. 1. 1.]
--- Stack 1/3
--- Stack 2/3
--- Stack 3/3
--- Required computational time: 0:00:04.960164

*** Two-step S2V-Registration and SRR Reconstruction ***

*** Slice-to-Volume Registration ***
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 1/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 2/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 3/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 4/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 5/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 6/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 7/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 8/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 9/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 10/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 11/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 12/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 13/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 14/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 15/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 16/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 17/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 18/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 1/3 (T2_bias) -- Slice 19/19
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 1/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 2/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 3/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 4/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 5/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 6/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 7/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 8/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 9/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 10/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 11/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 12/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 13/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 14/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 15/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 16/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 2/3 (T2_bias) -- Slice 17/17
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (T2_bias) -- Slice 1/21
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (T2_bias) -- Slice 2/21
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (T2_bias) -- Slice 3/21
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (T2_bias) -- Slice 4/21
Killed
`

Hi renbem,
when I used the command 'niftymic_run_reconstruction_pipeline ' , there were something wrong in the last step to reconstruct a srr_template_mask in template space. I could't sovle it.😭 I used the docker and pull your image.

The log prompt me that the motion_correction file is missing, but I have repeatedly confirmed that the file is in the current directory, or in the srr20 directory, everything is complete. All files are accessible with permission.

niftymic_reconstruct_volume_from_slices \

--filenames 'FetusNEWLIUYING_seg.nii.gz' 'FetusNEWLIUYINGA_seg.nii.gz' 'FetusNEWLIUYINGB_seg.nii.gz'
--dir-input-mc 'srr22/recon_template_space/motion_correction'
--output 'srr22/recon_template_space/srr_template_mask.nii.gz'
--reconstruction-space 'srr22/recon_template_space/srr_template.nii.gz'
--suffix-mask ''
--log-config 1
--mask
--sda
--alpha 1

*** Configuration: ***
--- alpha: 1.0
--- config: None
--- data_loss: linear
--- data_loss_scale: 1
--- dir_input_mc: srr22/recon_template_space/motion_correction
--- extra_frame_target: 10
--- filenames:
FetusNEWLIUYING_seg.nii.gz
FetusNEWLIUYINGA_seg.nii.gz
FetusNEWLIUYINGB_seg.nii.gz
--- filenames_masks: None
--- intensity_correction: 1
--- isotropic_resolution: None
--- iter_max: 10
--- iterations: 15
--- log_config: 1
--- mask: True
--- minimizer: lsmr
--- output: srr22/recon_template_space/srr_template_mask.nii.gz
--- pd_alg_type: ALG2
--- reconstruction_space: srr22/recon_template_space/srr_template.nii.gz
--- reconstruction_type: TK1L2
--- rho: 0.1
--- sda: True
--- slice_thicknesses: None
--- suffix_mask:
--- target_stack: None
--- tv_solver: PD
--- use_masks_srr: 0
--- verbose: 0
--- viewer: itksnap

NiftyMIC version: 0.7.5

--- File written to 'srr22/recon_template_space/config_reconstruct_volume_from_slices_20200625-142804.json'.

*** Read Data ***
--- Stack 'FetusNEWLIUYING_seg': Slice positions updated (15/15 slices deleted)
--- Stack 'FetusNEWLIUYING_seg' removed as all slices were deleted
--- Stack 'FetusNEWLIUYINGA_seg': Slice positions updated (15/15 slices deleted)
--- Stack 'FetusNEWLIUYINGA_seg' removed as all slices were deleted
--- Stack 'FetusNEWLIUYINGB_seg': Slice positions updated (19/19 slices deleted)
--- Stack 'FetusNEWLIUYINGB_seg' removed as all slices were deleted
Traceback (most recent call last):
File "/usr/local/bin/niftymic_reconstruct_volume_from_slices", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume_from_slices')()
File "/app/NiftyMIC/niftymic/application/reconstruct_volume_from_slices.py", line 127, in main
data_reader.read_data()
File "/app/NiftyMIC/niftymic/base/data_reader.py", line 286, in read_data
motion_updater.run()
File "/app/NiftyMIC/niftymic/utilities/motion_updater.py", line 225, in run
"All stacks removed. "
RuntimeError: All stacks removed. Did you check that the correct motion-correction directory was provided?

Hi, we started using your library and we are really pleased with the results. What a great package!

We have tested NiftyMIC on multiple MR T1 post contrast series of patients with brain metastases. Our main case is to reconstruct high-resolution 3D series from three orthogonal 2D projections with spacings between slices up to 8mm. The reconstructed images we received are great, but the processing lasted up to 2 hours for some data:

reconstruct_volume | Computational Time for Data Preprocessing: 0:00:01.133244
reconstruct_volume | Computational Time for Registrations: 0:34:09.471221
reconstruct_volume | Computational Time for Reconstructions: 1:24:53.866190
reconstruct_volume | Computational Time for Entire Reconstruction Pipeline: 2:00:46.653255

Is it possible to speed up the pipeline somehow e.g. by tuning the input parameters? Do you have any advice from your experience?

Hi.

I'm trying to set up a protocol for usage of NiftyMic.
Is there a rule of thumbs regarding the ratio of the slice thickness and the in plane resolution?
Also I'm curious whether the final reconstructed volume will follow the SNR of the thick images.
For example, if you have a thin soure image, then generate thick slice reformats in 3 orthognal planes (obviously will have better SNR than original thin image), will the resulting volume from NiftyMic processing have better SNR than the original thin image?

Best,
Ho-Joon Lee

I'm using with great interest your tool using the virtual machine distribution.
I'm currently having trouble reconstructing a good image since a lot of my results are far from optimal.
I'm using now 3 single stacks (one axial, one coronal and one sagittal). I was wondering if it is recommended to use more than one stack per orientation or the tool performs better given only 3 stacks. Also how does this impact the performance on my machine? I'm running on a 32gb i7 computer.

Thank you very much!

Gma

Dear all,

Thank you for this great package. I was wondering if the N4 bias field correction in the preprocessing step was a 3D one performed on the stack volume or a 2D one performed slice by slice.
Have a great day
Alex

Please feel free to delete this if this is the wrong place to post this.

The goal: Want to combine an axial and saggital volume into a single high res volume.

The issue: Permission error when running the docker image.

Traceback (most recent call last):
File "/usr/local/bin/niftymic_reconstruct_volume_from_slices", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume_from_slices')()
File "/app/NiftyMIC/niftymic/application/reconstruct_volume_from_slices.py", line 106, in main
input_parser.log_config(os.path.abspath(file))
File "/app/NiftyMIC/niftymic/utilities/input_arparser.py", line 170, in log_config
ph.write_dictionary_to_json(dic, path_to_config_file, verbose=True)
File "/usr/local/lib/python3.6/site-packages/pysitk/python_helper.py", line 1691, in write_dictionary_to_json
with open(path_to_file, access_mode) as fp:
PermissionError: [Errno 13] Permission denied: 'config_reconstruct_volume_from_slices_20220103-090401.json'

The command:
docker run -ti --rm -u $(id -u) -v $(pwd -P)/data -v $(pwd -P)/results renbem/niftymic niftymic_reconstruct_volume_from_slices --filenames ax.nii.gz sag.nii.gz --filenames-masks ax_mask.nii.gz sag_mask.nii.gz --output srr.nii.gz

I have tried to change the command various ways to no avail. For instance, omitting the -u flag throws the strange output.

--- File written to 'config_reconstruct_volume_from_slices_20220103-091200.json'.

*** Read Data ***
Traceback (most recent call last):
File "/usr/local/bin/niftymic_reconstruct_volume_from_slices", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume_from_slices')()
File "/app/NiftyMIC/niftymic/application/reconstruct_volume_from_slices.py", line 127, in main
data_reader.read_data()
File "/app/NiftyMIC/niftymic/base/data_reader.py", line 271, in read_data
extract_slices=self._extract_slices,
File "/app/NiftyMIC/niftymic/base/stack.py", line 60, in from_filename
raise exceptions.FileNotExistent(file_path)
niftymic.base.exceptions.FileNotExistent: File 'ax.nii.gz' does not exist

The file ax.nii.gz does indeed exist in the data dir specificed with -v.

Am I missing something obvious?

Hi, I try to install ITK_NiftyMIC following the instructions on this page (https://github.com/gift-surg/ITK_NiftyMIC/wiki).

Then I encountered following error when make -j8

[ 36%] Built target ITKIOSpatialObjects-all
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMFactoryBase.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMItpackSparseMatrix.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLightObject.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLinearSystemWrapper.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLinearSystemWrapperDenseVNL.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLinearSystemWrapperItpack.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLinearSystemWrapperVNL.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadBC.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadBCMFC.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadBase.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadEdge.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadElementBase.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadGrav.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadNoisyLandmark.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadLandmark.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadNode.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMLoadPoint.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMMaterialBase.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMMaterialLinearElasticity.cxx.o
[ 36%] Building CXX object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/itkFEMUtility.cxx.o
[ 36%] Building C object Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/dsrc2c.c.o
[ 36%] Linking CXX shared library ../../../../lib/libITKFEM-4.13.so
[ 36%] Built target ITKFEM
Scanning dependencies of target ITKFEM-all
[ 36%] Built target ITKFEM-all
[ 36%] Linking CXX shared library ../../../../lib/libITKIOMesh-4.13.so
[ 36%] Built target ITKIOMesh
Scanning dependencies of target ITKIOMesh-all
[ 36%] Built target ITKIOMesh-all
[ 36%] Linking CXX executable ../../../../bin/itkTestDriver
[ 36%] Built target itkTestDriver
Scanning dependencies of target ITKTestKernel-all
[ 36%] Built target ITKTestKernel-all
-- Using src='https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz'
-- Using src='https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz'
CMake Error at castxml-stamp/download-castxml.cmake:157 (message):
Each download failed!

error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=48d812ca105d7aa10fdc2d16678f7388&name=castxml-linux.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---

Wrapping/Generators/CastXML/CMakeFiles/castxml.dir/build.make:89: recipe for target 'Wrapping/Generators/CastXML/castxml-prefix/src/castxml-stamp/castxml-download' failed
make[2]: *** [Wrapping/Generators/CastXML/castxml-prefix/src/castxml-stamp/castxml-download] Error 1
CMakeFiles/Makefile2:14226: recipe for target 'Wrapping/Generators/CastXML/CMakeFiles/castxml.dir/all' failed
make[1]: *** [Wrapping/Generators/CastXML/CMakeFiles/castxml.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
CMake Error at PCRE-stamp/download-PCRE.cmake:157 (message):
Each download failed!

error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---
     error: downloading 'https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 50.58.123.181...

TCP_NODELAY set

Connected to midas3.kitware.com (50.58.123.181) port 443 (#0)

ALPN, offering http/1.1

successfully set certificate verify locations:

CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client hello (1):

[213 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server hello (2):

[93 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Certificate (11):

[2506 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server key exchange (12):

[333 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Server finished (14):

[4 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

[70 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS change cipher, Client hello (1):

[1 bytes data]

[5 bytes data]

TLSv1.2 (OUT), TLS handshake, Finished (20):

[16 bytes data]

[5 bytes data]

[5 bytes data]

TLSv1.2 (IN), TLS handshake, Finished (20):

[16 bytes data]

SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256

ALPN, server did not agree to a protocol

Server certificate:

subject: C=US; ST=New York; L=Clifton Park; O=Kitware, Inc.; CN=.kitware.com
start date: Aug 17 00:00:00 2017 GMT
expire date: Nov 12 12:00:00 2020 GMT
subjectAltName: host "midas3.kitware.com" matched cert's ".kitware.com"
issuer: C=US; O=DigiCert Inc; CN=DigiCert SHA2 Secure Server CA
SSL certificate verify ok.

[5 bytes data]

GET
/midas/api/rest?method=midas.bitstream.download&checksum=890c808122bd90f398e6bc40ec862102&name=pcre-8.40.tar.gz
HTTP/1.1

Host: midas3.kitware.com

User-Agent: curl/7.58.0

Accept: /

[5 bytes data]

The requested URL returned error: 404 Not Found

stopped the pause stream!

Closing connection 0

[5 bytes data]

TLSv1.2 (OUT), TLS alert, Client hello (1):

[2 bytes data]

     --- LOG END ---

Wrapping/Generators/SwigInterface/CMakeFiles/PCRE.dir/build.make:89: recipe for target 'Wrapping/Generators/SwigInterface/PCRE-prefix/src/PCRE-stamp/PCRE-download' failed
make[2]: *** [Wrapping/Generators/SwigInterface/PCRE-prefix/src/PCRE-stamp/PCRE-download] Error 1
CMakeFiles/Makefile2:14171: recipe for target 'Wrapping/Generators/SwigInterface/CMakeFiles/PCRE.dir/all' failed
make[1]: *** [Wrapping/Generators/SwigInterface/CMakeFiles/PCRE.dir/all] Error 2

For future proofing etc., it would be great to start having tagged releases of NIftyMIC & co.

This would also allow storing large binary files as part of the release assets on GitHub:
https://help.github.com/articles/distributing-large-binaries/

Ideally, the virtual box would sit there as well. However, it would need cutting down its size below 2Gb. Might this be feasible by using a minimalistic OS in it? For example Bodhi linux + virtual box seems to fit in 600Mb: https://www.osboxes.org/bodhi-linux/

Or even smaller:

• https://virtualboxes.org/images/tiny-core-linux/
• https://virtualboxes.org/images/lubuntu/

How much does all the rest take?

• currently, input file masks are converted to integer images automatically
• however, input file mask should be binary mask only (currently not ensured/tested)

Hi, I have included two reconstructed images here from our highly motion corrupted 2D T2-HASTE slices. I compared the images with BTK generated ones. I reconstructed those outputs in two steps:

1. niftymic_reconstruct_volume
   --filenames path-to-stack1.nii.gz ... path-to-stackN.nii.gz
   --filenames-masks path-to-stack1_mask.nii.gz ... path-to-stackN_mask.nii.gz
   --output path-to-srr.nii.gz \

2. niftymic_reconstruct_volume_from_slices
   --filenames path-to-stack1.nii.gz ... path-to-stackN.nii.gz
   --dir-input-mc dir-to-motion_correction
   --output path-to-srr.nii.gz
   --reconstruction-type HuberL2
   --alpha 0.003
   I used the brain+badslice mask for the first step.

For both of the data, by qualitative observation the reconstruction is not optimal. Do you have any suggestion or explanation for that? We actually intend to publish our study soon.

Hello,

Just a heads up that some math rendering is not working on my device (macOS, Chrome):

Hi NiftyMIC team,

I am a postdoc within the Posner lab trying to download NiftyMIC from source with the eventual goal of creating a GUI for reconstruction for use by clinical researchers without computational experience. Since the last ReadME update, it appears that the most recent versions of the libraries and dependencies used are no longer compatible. Is it possible to get a list of the versions of these used in the stable version of NiftyMIC.

Thank you for your consideration,

Meredith

Hello,

This is excellent work. Nice the reconstruction performance.
I want to simulate some corruption stacks, but I can't find the "niftymic.prototyping.simulator_slice_acqusition.py".

Thanks!

Hello,
Before all, thank you for this very nice toolbox.

I was a bit confused by the script niftymic_run_reconstruction_pipeline. In particular, in

Hi, I want to simulate the motion corrupted stacks of 2D slices, because I already have the SR images. How to do this.
Thanks!

Hello! First off, thanks for this software!

Sorry if this is inappropriate for Github issues, but my problem is probably not so much an issue with the code as a request for reconstruction parameters.

The attached image is my current best reconstruction from 3 acquisitions -- 1.6 x 1.6 x 5mm, 1.6 x 5 x 1.6mm, and 5 x 1.6 x 1.6mm (i.e a sagittal 2d, a coronal 2d, and an axial 2d). To my knowledge there is no slice gap. The brain scans I'm using are from an adult. I used only niftymic_reconstruct_volume, with parameters --reconstruction-type HuberL2 --isotropic-resolution 1.6 --interleave 1.

As you can see, there is a certain variation in intensity across slices, especially along the A/P direction. I'm not sure if this intensity variation affects the whole slice. I just started a run with --intensity-correction 0, just in case this is the issue. The parameters mentioned above all helped to lessen this effect, but it's still there.

I saw another user in the issues saying that he had good results in a similar use case, but with 8mm slices. So I feel that if I had a better idea of what parameters to use, I could probably achieve better results.

Also, I have multiple subjects with the same type of scans, and they all experience this banding.

Thank you so much for reading! Let me know if it would be helpful to give some more details.

I have been trying to make a reconstruction on the virtual box, but ran into an error at the Slice Outlier rejection.
I can imagine it is a memory error, since my memory was already at 97% up to this point.
If that is indeed the case, I can hopefully fix it by expanding my memory. But otherwise, perhaps I need to change some settings.
I ran it with a resolution of 2.0 mm as a first test if the code worked.

Thanks in advance.

The output is as follows (last part of running and the error):

--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 30/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 31/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 32/33
--- Cycle 1/3: Slice-to-Volume Registration -- Stack 3/3 (cor) -- Slice 33/33

*** Slice Outlier Rejection (NCC < 0.5) ***
Traceback (most recent call last):
File "/home/niftymic/Software/PythonVirtualenv/py3venv/bin/niftymic_reconstruct_volume", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume')()
File "/home/niftymic/Software/NiftyMIC/niftymic/application/reconstruct_volume.py", line 450, in main
two_step_s2v_reg_recon.run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 64, in run
self._run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/volumetric_reconstruction_pipeline.py", line 596, in _run
outlier_rejector.run()
File "/home/niftymic/Software/NiftyMIC/niftymic/utilities/outlier_rejector.py", line 56, in run
residual_evaluator.compute_slice_projections()
File "/home/niftymic/Software/NiftyMIC/niftymic/validation/residual_evaluator.py", line 170, in compute_slice_projections
self._reference, slice)
File "/home/niftymic/Software/NiftyMIC/niftymic/reconstruction/linear_operators.py", line 167, in A
stack_slice.sitk, interpolator=interpolator_mask)
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 933, in get_resampled_stack
image_sitk_mask=resampled_stack_sitk_mask,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 332, in from_sitk_image
slice_thickness=slice_thickness,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/stack.py", line 1278, in _extract_slices
slice_thickness=slice_thickness,
File "/home/niftymic/Software/NiftyMIC/niftymic/base/slice.py", line 59, in from_sitk_image
slice.sitk_mask = sitk.Cast(slice_sitk_mask, sitk.sitkUInt8)
File "/home/niftymic/Software/PythonVirtualenv/py3venv/lib/python3.6/site-packages/SimpleITK/SimpleITK.py", line 10215, in Cast
return _SimpleITK.Cast(image, pixelID)
RuntimeError: Exception thrown in SimpleITK Cast: /tmp/SimpleITK-build/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:399:
itk::ERROR: MultiThreader(0x386762c60): Exception occurred during SingleMethodExecute
/tmp/SimpleITK-build/ITK/Modules/Core/Common/src/itkMultiThreaderPThreads.cxx:187:
itk::ERROR: MultiThreader(0x386762c60): Unable to join thread.

Hi, great work! Which is the motion simulation code.

Hi,

I am using the docker image and am trying to generate a reconstructed volume of two sets of MRI dataset and I am using the niftymic_reconstruct_volume_from_slices. The reconstruction is done successfully. However, when the code tries to save the image, I receive a "Bus error" without any extra explanation. I mounted a host directory and checked the permission for writing from a container. All permission and write accesses are in place. Could you please help me understand what the possible sources of this bus error are and how I can resolve them.

Thank you very much for your help.

Best,
Iman

Hello,

Thanks for this great tool. Do the stacks have to be in a certain order according to acquisition. I am getting the error that there is not enough correspondence between stack02 and stack 01 or stack02 and stack04 for the rigid registration. Thanks!

Best,
Alex

Is there a Windows version?

Hello,

Thanks for this great tool. I am running into a permissions issue using as a Singularity container using the latest pull:

PermissionError: [Errno 13] Permission denied: '/app/NiftyMIC/MONAIfbs/monaifbs/models/checkpoint_dynUnet_DiceXent.pt'

Thanks for any ideas!

A new sub-module will be included in the package to perform the automated segmentation of brain in fetal MRI.
This module will be developed using the MONAI framework (https://monai.io/) and will provide:

• A new pretrained model that improves the performance of the currently used one
• The associated python script to run inference with the provided model
• Utilities to (re-)train the segmentation model to ease the introduction and use of model updates within the package.

Hi there,

I get the following errors even when launching simply (for instance) niftymic_reconstruct_volume:

niftymic_reconstruct_volume_from_slices
itkStreamingProcessObject not found in module ITKCommon because of exception:
'module' object has no attribute 'itkStreamingProcessObject'
itkMultiThreaderBase not found in module ITKCommon because of exception:
'module' object has no attribute 'itkMultiThreaderBase'
itkPoolMultiThreader not found in module ITKCommon because of exception:
'module' object has no attribute 'itkPoolMultiThreader'
itkPlatformMultiThreader not found in module ITKCommon because of exception:
'module' object has no attribute 'itkPlatformMultiThreader'
itkVectorContainerULSS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkVectorContainerULSS'
vectoritkImageRGBUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageRGBUC2'
vectoritkImageRGBAUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageRGBAUC2'
vectoritkImageVF22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF22'
vectoritkImageVF32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF32'
vectoritkImageVF42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF42'
vectoritkImageCVF22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF22'
vectoritkImageCVF32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF32'
vectoritkImageCVF42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF42'
vectoritkImageSS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageSS2'
vectoritkImageUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUC2'
vectoritkImageUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUS2'
vectoritkImageF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageF2'
vectoritkImageCF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCF2'
vectoritkImageVD22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD22'
vectoritkImageVD32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD32'
vectoritkImageVD42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD42'
vectoritkImageD2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageD2'
vectoritkImageUL2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUL2'
vectoritkImageULL2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageULL2'
vectoritkImageB2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageB2'
vectoritkImageFAF22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageFAF22'
vectoritkImageO22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageO22'
vectoritkImageSSRTD22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageSSRTD22'
vectoritkImageRGBUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageRGBUC3'
vectoritkImageRGBAUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageRGBAUC3'
vectoritkImageVF23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF23'
vectoritkImageVF33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF33'
vectoritkImageVF43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF43'
vectoritkImageCVF23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF23'
vectoritkImageCVF33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF33'
vectoritkImageCVF43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVF43'
vectoritkImageSS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageSS3'
vectoritkImageUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUC3'
vectoritkImageUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUS3'
vectoritkImageF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageF3'
vectoritkImageCF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCF3'
vectoritkImageVD23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD23'
vectoritkImageVD33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD33'
vectoritkImageVD43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD43'
vectoritkImageD3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageD3'
vectoritkImageUL3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageUL3'
vectoritkImageULL3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageULL3'
vectoritkImageB3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageB3'
vectoritkImageFAF33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageFAF33'
vectoritkImageO33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageO33'
vectoritkImageSSRTD33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageSSRTD33'
vectoritkImageVF12 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF12'
vectoritkImageVD24 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD24'
vectoritkImageVD34 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD34'
vectoritkImageVD44 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVD44'
vectoritkImageVF13 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageVF13'
vectoritkImageCVD22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD22'
vectoritkImageCVD32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD32'
vectoritkImageCVD42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD42'
vectoritkImageCVD23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD23'
vectoritkImageCVD33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD33'
vectoritkImageCVD43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'vectoritkImageCVD43'
itkImageToImageFilterISS2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterISS2ICF2'
itkImageToImageFilterISS3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterISS3ICF3'
itkImageToImageFilterIUC2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterIUC2ICF2'
itkImageToImageFilterIUC3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterIUC3ICF3'
itkImageToImageFilterIUS2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterIUS2ICF2'
itkImageToImageFilterIUS3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterIUS3ICF3'
itkImageToImageFilterICF2ISS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF2ISS2'
itkImageToImageFilterICF3ISS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF3ISS3'
itkImageToImageFilterICF2IUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF2IUC2'
itkImageToImageFilterICF3IUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF3IUC3'
itkImageToImageFilterICF2IUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF2IUS2'
itkImageToImageFilterICF3IUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterICF3IUS3'
itkImageToImageFilterISSRTD22ISSRTD22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterISSRTD22ISSRTD22'
itkImageToImageFilterISSRTD33ISSRTD33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageToImageFilterISSRTD33ISSRTD33'
itkInPlaceImageFilterIRGBUC2ISS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC2ISS2'
itkInPlaceImageFilterIRGBUC3ISS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC3ISS3'
itkInPlaceImageFilterIRGBUC2IUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC2IUS2'
itkInPlaceImageFilterIRGBUC3IUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC3IUS3'
itkInPlaceImageFilterIRGBUC2IF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC2IF2'
itkInPlaceImageFilterIRGBUC3IF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIRGBUC3IF3'
itkInPlaceImageFilterISS2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterISS2ICF2'
itkInPlaceImageFilterISS3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterISS3ICF3'
itkInPlaceImageFilterIUC2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIUC2ICF2'
itkInPlaceImageFilterIUC3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIUC3ICF3'
itkInPlaceImageFilterIUS2ICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIUS2ICF2'
itkInPlaceImageFilterIUS3ICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterIUS3ICF3'
itkInPlaceImageFilterICF2ISS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF2ISS2'
itkInPlaceImageFilterICF3ISS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF3ISS3'
itkInPlaceImageFilterICF2IUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF2IUC2'
itkInPlaceImageFilterICF3IUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF3IUC3'
itkInPlaceImageFilterICF2IUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF2IUS2'
itkInPlaceImageFilterICF3IUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkInPlaceImageFilterICF3IUS3'
itkDefaultDynamicMeshTraitsSS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS2'
itkDefaultDynamicMeshTraitsSS22SSSS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS22SSSS'
itkDefaultDynamicMeshTraitsSS22SSSSSS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS22SSSSSS'
itkDefaultDynamicMeshTraitsUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC2'
itkDefaultDynamicMeshTraitsUC22UCUC not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC22UCUC'
itkDefaultDynamicMeshTraitsUC22UCUCUC not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC22UCUCUC'
itkDefaultDynamicMeshTraitsUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS2'
itkDefaultDynamicMeshTraitsUS22USUS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS22USUS'
itkDefaultDynamicMeshTraitsUS22USUSUS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS22USUSUS'
itkDefaultDynamicMeshTraitsF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsF2'
itkDefaultDynamicMeshTraitsD2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsD2'
itkDefaultDynamicMeshTraitsSS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS3'
itkDefaultDynamicMeshTraitsSS33SSSS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS33SSSS'
itkDefaultDynamicMeshTraitsSS33SSSSSS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsSS33SSSSSS'
itkDefaultDynamicMeshTraitsUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC3'
itkDefaultDynamicMeshTraitsUC33UCUC not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC33UCUC'
itkDefaultDynamicMeshTraitsUC33UCUCUC not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUC33UCUCUC'
itkDefaultDynamicMeshTraitsUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS3'
itkDefaultDynamicMeshTraitsUS33USUS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS33USUS'
itkDefaultDynamicMeshTraitsUS33USUSUS not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsUS33USUSUS'
itkDefaultDynamicMeshTraitsF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsF3'
itkDefaultDynamicMeshTraitsD3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultDynamicMeshTraitsD3'
itkDefaultStaticMeshTraitsSS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsSS2'
itkDefaultStaticMeshTraitsUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsUC2'
itkDefaultStaticMeshTraitsUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsUS2'
itkDefaultStaticMeshTraitsF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsF2'
itkDefaultStaticMeshTraitsD2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsD2'
itkDefaultStaticMeshTraitsSS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsSS3'
itkDefaultStaticMeshTraitsUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsUC3'
itkDefaultStaticMeshTraitsUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsUS3'
itkDefaultStaticMeshTraitsF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsF3'
itkDefaultStaticMeshTraitsD3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkDefaultStaticMeshTraitsD3'
itkImageDuplicatorISSRTD22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageDuplicatorISSRTD22'
itkImageDuplicatorISSRTD33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageDuplicatorISSRTD33'
itkImageSinkIRGBUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIRGBUC2'
itkImageSinkIRGBUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIRGBUC3'
itkImageSinkIRGBAUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIRGBAUC2'
itkImageSinkIRGBAUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIRGBAUC3'
itkImageSinkIVF22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF22'
itkImageSinkIVF23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF23'
itkImageSinkIVF32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF32'
itkImageSinkIVF33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF33'
itkImageSinkIVF42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF42'
itkImageSinkIVF43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIVF43'
itkImageSinkICVF22 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF22'
itkImageSinkICVF23 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF23'
itkImageSinkICVF32 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF32'
itkImageSinkICVF33 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF33'
itkImageSinkICVF42 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF42'
itkImageSinkICVF43 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICVF43'
itkImageSinkISS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkISS2'
itkImageSinkISS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkISS3'
itkImageSinkIUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIUC2'
itkImageSinkIUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIUC3'
itkImageSinkIUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIUS2'
itkImageSinkIUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIUS3'
itkImageSinkIF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIF2'
itkImageSinkIF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkIF3'
itkImageSinkICF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICF2'
itkImageSinkICF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkICF3'
itkImageSinkVISS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVISS2'
itkImageSinkVIUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIUC2'
itkImageSinkVIUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIUS2'
itkImageSinkVIF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIF2'
itkImageSinkVISS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVISS3'
itkImageSinkVIUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIUC3'
itkImageSinkVIUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIUS3'
itkImageSinkVIF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkImageSinkVIF3'
itkNumericTraitsCF not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkNumericTraitsCF'
itkPointSetSS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetSS2'
itkPointSetUC2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetUC2'
itkPointSetUS2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetUS2'
itkPointSetF2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetF2'
itkPointSetD2 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetD2'
itkPointSetSS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetSS3'
itkPointSetUC3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetUC3'
itkPointSetUS3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetUS3'
itkPointSetF3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetF3'
itkPointSetD3 not loaded from module ITKCommon because of exception:
'module' object has no attribute 'itkPointSetD3'
Traceback (most recent call last):
File "/usr/local/bin/niftymic_reconstruct_volume_from_slices", line 11, in
load_entry_point('NiftyMIC', 'console_scripts', 'niftymic_reconstruct_volume_from_slices')()
File "/home/zappst/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/zappst/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 2852, in load_entry_point
return ep.load()
File "/home/zappst/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 2443, in load
return self.resolve()
File "/home/zappst/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 2449, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/zappst/NiftyMIC-master/niftymic/application/reconstruct_volume_from_slices.py", line 21, in
import niftymic.reconstruction.admm_solver as admm
File "/home/zappst/NiftyMIC-master/niftymic/reconstruction/admm_solver.py", line 19, in
from niftymic.reconstruction.solver import Solver
File "/home/zappst/NiftyMIC-master/niftymic/reconstruction/solver.py", line 21, in
import niftymic.reconstruction.linear_operators as lin_op
File "/home/zappst/NiftyMIC-master/niftymic/reconstruction/linear_operators.py", line 26, in
class LinearOperators(object):
File "/home/zappst/NiftyMIC-master/niftymic/reconstruction/linear_operators.py", line 48, in LinearOperators
image_type=itk.Image.D3,
File "/home/zappst/.local/lib/python2.7/site-packages/itkLazy.py", line 52, in getattribute
itkBase.LoadModule(module, namespace)
File "/home/zappst/.local/lib/python2.7/site-packages/itkBase.py", line 214, in LoadModule
namespace[snakeCaseFunction] = getattr(module, snakeCaseFunction)
AttributeError: 'module' object has no attribute 'image_to_image_filter'

I tried to reinstall it. All requirements are met and all prerequisites from the GitHub website.
I was wondering what else I can try.

Many thanks,
Stefano.

niftymic_run_reconstruction_pipeline
--filenames
nifti/name-of-stack-1.nii.gz
nifti/name-of-stack-2.nii.gz
nifti/name-of-stack-N.nii.gz
--filenames-masks
seg/name-of-stack-1.nii.gz
seg/name-of-stack-2.nii.gz
seg/name-of-stack-N.nii.gz
--dir-output srr

This command does not work. There is no --filenames-masks or --dir-output anymore. I tried this:
niftymic_run_reconstruction_pipeline
--filenames
nifti/name-of-stack-1.nii.gz
seg/name-of-stack-1.nii.gz
--output srr/name-of-stack-1.nii.gz

This works, but there is no benefit of reconstruction. Maybe I should run it three times and use the xyz direction output to reconstruct it?

I installed NiftyMIC as vm on VirtualBox two months ago and i used it since that moment without any major problem. However in this last week i got this warning:

** "The volume "filesystem root" has only X bytes disk space remaining".**

Now i have 0 bytes disk space remaining and i can't elaborate any images.

Executing the following command i obtain:

What can i do?

Hello,

I have started using Niftymic very recently, more precisely the registration.
The output file given contains the transformation. The transformed image itself, which is the one I need, was a bit harder to find, as it is sent to the temporary files. I was wondering if it would be possible to implement a solution to choose in which file to send the registered image instead of the transformation.

Thanks !