Open valosekj opened 1 month ago
Debugging sub-1836B6029B_ses-1836B_acq-ZOOMit_dir-AP_dwi.nii.gz
: there is a complete signal loss at the bottom part of the image (around C7) (consistent with the original publication). Cropping the last 6 slices resolves the crashing sct_dmri_moco
:
sct_crop_image -i "${file_dwi}_crop".nii.gz -zmin 6 -zmax -1 -o "${file_dwi}_crop_crop".nii.gz
Change pushed in https://github.com/valosekj/dcm-brno/commit/f0df460a9de007672718f2be590948711c3eeb02
Cropping the last 6 slices resolves issues for a lot of subjects. Current log files are:
dcm-brno_2024-07-08/log$ ls -1 err*
err.01_process_data_sub-2249B4725B_ses-4725B.log
err.01_process_data_sub-2416B6027B_ses-2416B.log
err.01_process_data_sub-2481B6079B_ses-2481B.log
err.01_process_data_sub-2590B4647B_ses-4647B.log
err.01_process_data_sub-2773B4661B_ses-2773B.log
Changing the metric for sct_dmri_moco
to CC
helped for sub-2249B4725B_ses-4725B
and sub-2590B4647B_ses-4647B
.
Fixed in https://github.com/valosekj/dcm-brno/commit/cf162b86ae1be6a15eb722119652dc9b3c96b11d
sub-2416B6027B_ses-2416B
had disc labels for two runs under derivatives
.
Fixed in https://github.com/valosekj/dcm-brno_derivatives/commit/0415eb769bb4bb5531a7b1118f72b20a874b1f86
sub-2481B6079B_ses-2481B
has an empty SC seg; probably related to https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4556
I ran the prediction locally and pushed to derivatives
in https://github.com/valosekj/dcm-brno_derivatives/commit/b6e5d9ac65d2dc66a59427764144651e866c8f70
sub-2773B4661B_ses-2773B
finished with an error for sct_register_to_template
.
When trying the command locally, it worked fine, though.
Even after increasing the crop size to
35x35x0
(https://github.com/valosekj/dcm-brno/issues/14#issuecomment-2210748905),sct_dmri_moco
is still crashing for the following subjects.https://github.com/valosekj/dcm-brno/blob/905e734c803800963d1e39d2fed5babd1239c721/scripts/01_process_data.sh#L337-L341
Error logs for all the subjects:
details
```bash $ dcm-brno_2024-07-05/log$ for err in err*;do echo $err; tail -3 $err; echo "";done err.01_process_data_sub-1836B6029B_ses-1836B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x21cf840): Joint PDF summed to zero err.01_process_data_sub-1860B6472B_ses-6472B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x2b13cf0): Joint PDF summed to zero err.01_process_data_sub-2060B4733B_ses-2060B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x1f3bcf0): Joint PDF summed to zero err.01_process_data_sub-2249B4725B_ses-4725B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x24d2220): Joint PDF summed to zero err.01_process_data_sub-2295B4676B_ses-2295B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x315ae70): Joint PDF summed to zero err.01_process_data_sub-2295B4676B_ses-4676B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x2c0ee90): Joint PDF summed to zero err.01_process_data_sub-2330B6137B_ses-6137B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3659f20): Joint PDF summed to zero err.01_process_data_sub-2371B4687B_ses-4687B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x1f12c70): Joint PDF summed to zero err.01_process_data_sub-2372B2863B_ses-2372B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x38af280): Joint PDF summed to zero err.01_process_data_sub-2372B2863B_ses-2863B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x314bcf0): Joint PDF summed to zero err.01_process_data_sub-2407B5757B_ses-5757B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x296f670): Joint PDF summed to zero err.01_process_data_sub-2411B4591B_ses-2411B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x38c7af0): Joint PDF summed to zero err.01_process_data_sub-2416B6027B_ses-2416B.log File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/centerline/nurbs.py", line 103, in __init__ raise ArithmeticError('There are too few points to compute. The number of points of the curve must ' ArithmeticError: There are too few points to compute. The number of points of the curve must be strictly superior to degre + 2, in this case: 5. Either change degree to a lower value, or add points to the curve. err.01_process_data_sub-2417B4965B_ses-4965B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x36ae3a0): Joint PDF summed to zero err.01_process_data_sub-2418B4628B_ses-4628B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x1fa9170): Joint PDF summed to zero err.01_process_data_sub-2450B6177B_ses-2450B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x1e97d60): Joint PDF summed to zero err.01_process_data_sub-2450B6177B_ses-6177B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3d74690): Joint PDF summed to zero err.01_process_data_sub-2481B6079B_ses-2481B.log File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/cropping.py", line 116, in get_bbox_from_mask min(data_nonzero[0]), max(data_nonzero[0]), ValueError: min() arg is an empty sequence err.01_process_data_sub-2590B4647B_ses-2590B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3d33960): Joint PDF summed to zero err.01_process_data_sub-2590B4647B_ses-4647B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3517980): Joint PDF summed to zero err.01_process_data_sub-2773B4661B_ses-2773B.log File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/image.py", line 321, in __init__ raise ValueError("Image sform does not match qform") ValueError: Image sform does not match qform err.01_process_data_sub-2804B4632B_ses-4632B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3622c70): Joint PDF summed to zero err.01_process_data_sub-3782B6193B_ses-3782B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3048b70): Joint PDF summed to zero err.01_process_data_sub-3998B6406B_ses-3998B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x3286240): Joint PDF summed to zero err.01_process_data_sub-4891B6572B_ses-4891B.log File: /__w/build_ANTs/build_ANTs/antsbin/staging/include/ITK-5.1/itkMattesMutualInformationImageToImageMetricv4.hxx Line: 312 Description: itk::ERROR: MattesMutualInformationImageToImageMetricv4(0x2c02c70): Joint PDF summed to zero ```