file name bug in antsMultivariateTemplateConstruction.sh #1932
Description
Operating system and version
Linux
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
2.5.0-g592625b
ANTs installation type
Downloaded Github release binaries
Summary of the problem
When doing rigid body registration (-r 1), line 993 of antsMultivariateTemplateConstruction.sh sets up a call to ANTS to perform registration and sets the name of the output file based on the complete name of the input file. This means that ANTS will set the name of the *Affine.txt file it generates based on the the complete name of the input file.
Unfortunately, in line 1011 it assumes that the Affine.txt filename will be built from the name of the input file truncated at the first dot in the filname, as defined in line 1010.
In practice this means that if your input file is something like "participant1.nii.gz" you'll be fine. If it is something like "sub-10095-5cc9e675a43e5f00368a1fad-1.3.12.2.1107.5.2.43.67025.2019050111054255647402353.0.0.0.nii.gz" , though, then the call at line 1011 will want to use something like "rigid113_0_subj-sub-10095-5cc9e675a43e5f00368a1fad-1Affine.txt" (notice that the 'Affine.txt' is appended right after the first '.' in the input filename) and won't be able to find it, resulting in an error like this:
HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0
:
#000: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fdeprec.c line 156 in itk_H5Fis_hdf5(): unable to determine if file is accessible as HDF5
major: File accessibility
minor: Not an HDF5 file
#001: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3769 in itk_H5VL_file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#002: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3699 in H5VL__file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#003: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLnative_file.c line 384 in itk_H5VL__native_file_specific(): error in HDF5 file check
major: File accessibility
minor: Unable to initialize object
#004: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c line 1073 in itk_H5F__is_hdf5(): unable to open file
major: File accessibility
minor: Unable to initialize object
#005: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 723 in itk_H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#006: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = './rigid113_0_subj-sub-10095-5cc9e675a43e5f00368a1fad-1Affine.txt', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessibility
minor: Unable to open file
Exception caught during WarpImageMultiTransform.
itk::ExceptionObject (0x63e5f526b300)
Location: "unknown"
File: /home/runner/work/_temp/build/ITKv5/Modules/IO/TransformInsightLegacy/src/itkTxtTransformIO.cxx
Line: 122
Description: ITK ERROR: TxtTransformIOTemplate(0x63e5f52bb920): The file could not be opened for read access
Filename: "./rigid113_0_subj-sub-10095-5cc9e675a43e5f00368a1fad-1Affine.txt"
For what it's worth, antsMultivariateTemplateConstruction2.sh does not appear to have this bug.
Commands to reproduce the problem.
/opt/ants-2.5.0/bin/antsMultivariateTemplateConstruction.sh -j 7 -g 0.15 -d 3 -i 4 -m 1x0x0 -w 1 -n 1 -k 1 -o full_template_ -c 2 -s CC -r 1 -b 0 -t GR -y 1 /input/subj-*-*.nii.gz
Output of the command with verbose output.
--------------------------------------------------------------------------------------
Creating template full_template_template0.nii.gz from a population average image from the inputs.
/input/subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz /input/subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
--------------------------------------------------------------------------------------
bigimage 4 maxSize [176, 240, 256]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading /input/subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
reading /input/subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: /input/subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
Reference image: full_template_template0.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order):
1. ./initialCOM0_0_subj-YA2-5b9c141562d9320011f1084a-1.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: ./initialCOM0_0_subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
Using double precision for computations.
Input scalar image: /input/subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
Reference image: full_template_template0.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order):
1. ./initialCOM0_1_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: ./initialCOM0_1_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
bigimage 4 maxSize [176, 240, 256]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading ./initialCOM0_0_subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
reading ./initialCOM0_1_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
writing output
Sharpening method none
--------------------------------------------------------------------------------------
Starting ANTS rigid registration on max 7 cpucores.
Progress can be viewed in ./job*_metriclog.txt
--------------------------------------------------------------------------------------
Using max 7 parallel threads
Running sh ./job_00_r.sh
Running sh ./job_01_r.sh
AFFINE: ./rigid1_0_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6Affine.txt
moving_image_filename: /input/subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz components 1
output_image_filename: ./rigid1_0_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
reference_image_filename: full_template_template0.nii.gz
[0/1]: AFFINE: ./rigid1_0_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6Affine.txt
AFFINE: ./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1Affine.txt
moving_image_filename: /input/subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz components 1
output_image_filename: ./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
reference_image_filename: full_template_template0.nii.gz
[0/1]: AFFINE: ./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1Affine.txt
User Linear interpolation
You are doing something more complex -- we wont check syntax in this case
output origin: [118.686, 126.854, -87.7271]
output size: [176, 240, 256]
output spacing: [1.2, 1, 1]
output direction: -0.993915 0.0362486 -0.104017
-0.00966189 -0.969352 -0.245484
-0.109728 -0.242985 0.963804
User Linear interpolation
HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0:
#000: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fdeprec.c line 156 in itk_H5Fis_hdf5(): unable to determine if file is accessible as HDF5
major: File accessibility
minor: Not an HDF5 file
#001: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3769 in itk_H5VL_file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#002: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3699 in H5VL__file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#003: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLnative_file.c line 384 in itk_H5VL__native_file_specific(): error in HDF5 file check
major: File accessibility
minor: Unable to initialize object
#004: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c line 1073 in itk_H5F__is_hdf5(): unable to open file
major: File accessibility
minor: Unable to initialize object
#005: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 723 in itk_H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#006: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = './rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1Affine.txt', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessibility
minor: Unable to open file
Exception caught during WarpImageMultiTransform.
itk::ExceptionObject (0x634139bb9030)
Location: "unknown"
File: /home/runner/work/_temp/build/ITKv5/Modules/IO/TransformInsightLegacy/src/itkTxtTransformIO.cxx
Line: 122
Description: ITK ERROR: TxtTransformIOTemplate(0x634139c023e0): The file could not be opened for read access
Filename: "./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1Affine.txt"
HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0:
#000: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fdeprec.c line 156 in itk_H5Fis_hdf5(): unable to determine if file is accessible as HDF5
major: File accessibility
minor: Not an HDF5 file
#001: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3769 in itk_H5VL_file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#002: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLcallback.c line 3699 in H5VL__file_specific(): file specific failed
major: Virtual Object Layer
minor: Can't operate on object
#003: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5VLnative_file.c line 384 in itk_H5VL__native_file_specific(): error in HDF5 file check
major: File accessibility
minor: Unable to initialize object
#004: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c line 1073 in itk_H5F__is_hdf5(): unable to open file
major: File accessibility
minor: Unable to initialize object
#005: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 723 in itk_H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#006: /home/runner/work/_temp/build/ITKv5/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = './rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1Affine.txt', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessibility
minor: Unable to open file
AverageImages 3 full_template_template0.nii.gz 2 ./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz ./rigid1_0_subj-sub-10039-65f3468c7937a02e6668f4f2-1_3_12_2_1107_5_2_43_67025_2024031411344164356502353_0_0_0_anat-T1w_acq-mprage_20240314111132_6.nii.gz
Cannot read input file: ./rigid0_0_subj-YA2-5b9c141562d9320011f1084a-1.3.12.2.1107.5.2.43.67025.2018091412383081618797809.0.0.0.nii.gz
summarizeimageset: ERROR - output file full_template_template0.nii.gz could not be created
Data to reproduce the problem
Any T1w nifti files named as shown in the output above should suffice to reproduce this problem.