BUG: Nonrigid transform causes type error

[pvandyken]

Problem

When running a nonrigid transform using wm_register_to_atlas_new.py, it crashes as soon as it tries to save the results of its first iteration with the error: TypeError: 'float' object cannot be interpreted as an integer (see below for full trace).

Steps to reproduce

Environment

python==3.7.9
whitematteranalysis==0.3.0

Steps

1. Follow the steps in the parcellation tutorial, including downloading the example dataset, up until step 5: Tractography Registration.
2. Run the transform as indicated, but use -mode affine instead of -mode rigid_affine_fast. This step will work fine.
3. Run a second transform on the affine output using nonrigid:

wm_register_to_atlas_new.py -mode nonrigid TractRegistrationAffine/example-UKF-data/output_tractography/example-UKF-data_reg.vtk ORG-Atlases-1.1.1/ORG-RegAtlas-100HCP/registration_atlas.vtk TractRegistrationNonrigid

This produces the following output:

Importing whitematteranalysis package.


<register> =========GROUP REGISTRATION============
<register> Registering to atlas.
<register> Input  subject file:  TractRegistrationAffine/example-UKF-data/output_tractography/example-UKF-data_reg.vtk
<register> Input  atlas file:  ORG-Atlases-1.1.1/ORG-RegAtlas-100HCP/registration_atlas.vtk
<register> Output directory:  TractRegistrationNonrigid

<register> ============PARAMETERS=================
<register> Registration mode: nonrigid
<register> Number of fibers to analyze per subject:  20000
<register> Minimum length of fibers to analyze (in mm):  40
<register> Maximum  length of fibers to analyze (in mm):  260
<register> Verbose display and intermediate image saving OFF.

<register> Starting registration...

ADD PD: [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
UPDATE NONRIGID GRID:  4 648 ==> 192 OPTIMIZER: BFGS
TractRegistrationNonrigid/example-UKF-data_reg/log_subject_00001_iteration_00001_sigma_005_grid_004.log
EXCEPTION WAS CAUGHT, total objectives: 20
vtkBSplineTransform (0x2233730)
  Debug: Off
  Modified Time: 44752
  Reference Count: 1
  Registered Events: (none)
  Inverse: (0)
  InverseFlag: 0
  InverseTolerance: 1e-06
  InverseIterations: 500
  BorderMode: Zero
  DisplacementScale: 1


Traceback (most recent call last):
  File "/path/to/venv/bin/wm_register_to_atlas_new.py", line 372, in <module>
    main()
  File "/path/to/venv/bin/wm_register_to_atlas_new.py", line 345, in main
    register.iterate()
  File "/path/to/venv/lib/python3.7/site-packages/whitematteranalysis/congeal_to_atlas.py", line 143, in iterate
    wma.io.write_transforms_to_itk_format(tx_list, outdir, id_list)
  File "/path/to/venv/lib/python3.7/site-packages/whitematteranalysis/io.py", line 513, in write_transforms_to_itk_format
    for s in range(extent_0[0], extent_1[0]+1):
TypeError: 'float' object cannot be interpreted as an integer

Any assistance would be appreciated!

[ljod]

Hi we will try to reproduce this so we can see what is happening. Thank you for the report! We'll keep you posted.

[shivazadeh]

Hi, I'm getting the same error using python==3.7.10 and whitematteranalysis==0.3.0.

[zhangfanmark]

Hi @pvandyken @shivazadeh this issue should have been fixed with the new change. Let me know if you still have issues.