Open yuezhang9842 opened 2 years ago
Hi, if it's killed because of not enough memory, there's not much I can do, unfortunately. Besides having more RAM available, you could create tighter masks or lower the resolution, e.g. set --isotropic-resolution to 1.5 or 2 mm. Both will reduce the memory requirements. The latter of course will reduce image quality but could be a good first step to check that you can get successful recontructions
One thing though, Docker may have less memory available than what you have on your system. Perhaps worth checking as well.
Hello. The “killed” problem has been solved, it seems that the ARM64 system used by Apple M1 is not suitable for docker. So I switched to Windows. However I also wonder if I need to download the images of ITK_Niftymic and Simplereg to use Niftymic?
Meanwhile, I‘m having troubles with “Transformation to Template Space”. It seems that the registration was not successful. Here is my code:
niftymic_register_image \
--fixed ./NiftyMIC/data/templates/STA33.nii.gz \
--fixed-mask ./NiftyMIC/data/templates/STA33_mask.nii.gz \
--moving /www1/results/results-0.01-t/srr.nii.gz \
--moving-mask /www1/results/results-0.01-t/srr_mask.nii.gz \
--dir-input-mc /www1/results/results-0.01-t/motion_correction \
--output /www1/results/results-0.01-t/registration-transform.txt
niftymic_reconstruct_volume_from_slices \
--filenames /www1/cor/T2_bias.nii.gz /www1/sag/T2_bias.nii.gz /www1/tra/T2_bias.nii.gz \
--filenames-masks /www1/cor/T2_label.nii.gz /www1/sag/T2_label.nii.gz /www1/tra/T2_label.nii.gz \
--output /www1/results/srr-0.01-t-mc.nii.gz \
--reconstruction-space ./NiftyMIC/data/templates/STA33.nii.gz \
--reconstruction-type TK1L2 \
--alpha 0.01
***************************************************************************************************
*** Configuration: ***
--- config: None
--- dir_input_mc: /www1/results/results-0.01-t/motion_correction
--- fixed: ./NiftyMIC/data/templates/STA33.nii.gz
--- fixed_mask: ./NiftyMIC/data/templates/STA33_mask.nii.gz
--- init_pca: False
--- initial_transform: None
--- log_config: 1
--- method: RegAladin
--- moving: /www1/results/results-0.01-t/srr.nii.gz
--- moving_mask: /www1/results/results-0.01-t/srr_mask.nii.gz
--- output: /www1/results/results-0.01-t/registration-transform.txt
--- verbose: 0
NiftyMIC version: 0.9
***************************************************************************************************
--- File written to '/www1/results/results-0.01-t/config_register_image_20220619-153337.json'.
***************************************************************************************************
*** Read Data ***
***************************************************************************************************
*** Registration ***
--- Run Registration (RegAladin) ... done
--- Registration transformation written to '/www1/results/results-0.01-t/registration-transform.txt'
***************************************************************************************************
*** Update Motion-Correction Transformations ***
--- 0 transformations written to '/www1/results/results-0.01-t/motion_correction'
***************************************************************************************************
*** Summary ***
register_image | Computational Time: 0:00:15.605149
And here is the results of SRR, But I don‘t know what is the problem causing such strange results. Hope to get your help!!!
I met similar problem after SSRI. Did you solve this issue ? Thanks.
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 `