No GenericAffine.mat exist when running antsMultivariateTemplateConstruction2.sh

[Bamboo429]

Operating system and version

Ubuntu 20.04

CPU architecture

x86_64 (PC, Intel Mac, other Intel/AMD)

ANTs code version

ANTs Version: 2.5.1.post42-g35d9381

ANTs installation type

Compiled from source

Summary of the problem

Hi ANTs team,
I am running antsMultivariateTemplateConstruction2.sh but keep facing error message

I have tried to set the ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 but still the same error

However, if I run the command antsRegistration provided in job_00_r.sh, the program create the *Warp.nii.gz and *GenericAffine.mat successfully

Here is the full log file
job_0_metriclog.txt

Please let me know how can I fix it. Thank you so much!

Commands to reproduce the problem.

antsMultivariateTemplateConstruction2.sh -b 1 -d 3 -v 32 -a 0 -g 0.2 -i 20 -j 2 -c 2 -k 4 -n 0 -m MI /home/subjectList_2.csv

Output of the command with verbose output.

---

Multivariate template construction using the following 4-tuples:

/home/Reg_2/VT_00026_arterial_pc.nii.gz /home/Reg_2/VT_00026_vein_supp_arterial_sub.nii.gz /home/Reg_2/VT_00026_venous_pc.nii.gz /home/Reg_2/VT_00026_artery_supp_venous_sub.nii.gz
/home/Reg_2/VT_00007_arterial_pc.nii.gz /home/Reg_2/VT_00007_vein_supp_arterial_sub.nii.gz /home/Reg_2/VT_00007_venous_pc.nii.gz /home/Reg_2/VT_00007_artery_supp_venous_sub.nii.gz

---

Creating template antsBTPtemplate0.nii.gz from a population average image from the inputs.
/home/Reg_2/VT_00026_arterial_pc.nii.gz /home/Reg_2/VT_00007_arterial_pc.nii.gz

bigimage 4 maxSize [512, 512, 470]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading /home/Reg_2/VT_00026_arterial_pc.nii.gz
reading /home/Reg_2/VT_00007_arterial_pc.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: /home/Reg_2/VT_00026_arterial_pc.nii.gz
Reference image: antsBTPtemplate0.nii.gz

The composite transform comprises the following transforms (in order):

1. ./initialCOM0_0_VT_00026_arterial_pc.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM0_0_VT_00026_arterial_pc.nii.gz
   Using double precision for computations.
   Input scalar image: /home/Reg_2/VT_00007_arterial_pc.nii.gz
   Reference image: antsBTPtemplate0.nii.gz
   =============================================================================
   The composite transform comprises the following transforms (in order):
2. ./initialCOM0_1_VT_00007_arterial_pc.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM0_1_VT_00007_arterial_pc.nii.gz
   bigimage 4 maxSize [512, 512, 470]
   Setting physical space of output average image based on largest image
   Averaging 2 images with dim = 3 vector components 1
   reading ./initialCOM0_0_VT_00026_arterial_pc.nii.gz
   reading ./initialCOM0_1_VT_00007_arterial_pc.nii.gz
   writing output
   Sharpening method none

---

Creating template antsBTPtemplate1.nii.gz from a population average image from the inputs.
/home/Reg_2/VT_00026_vein_supp_arterial_sub.nii.gz /home/Reg_2/VT_00007_vein_supp_arterial_sub.nii.gz

bigimage 4 maxSize [512, 512, 470]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading /home/Reg_2/VT_00026_vein_supp_arterial_sub.nii.gz
reading /home/Reg_2/VT_00007_vein_supp_arterial_sub.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: /home/Reg_2/VT_00026_vein_supp_arterial_sub.nii.gz
Reference image: antsBTPtemplate1.nii.gz

The composite transform comprises the following transforms (in order):

1. ./initialCOM1_0_VT_00026_vein_supp_arterial_sub.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM1_0_VT_00026_vein_supp_arterial_sub.nii.gz
   Using double precision for computations.
   Input scalar image: /home/Reg_2/VT_00007_vein_supp_arterial_sub.nii.gz
   Reference image: antsBTPtemplate1.nii.gz
   =============================================================================
   The composite transform comprises the following transforms (in order):
2. ./initialCOM1_1_VT_00007_vein_supp_arterial_sub.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM1_1_VT_00007_vein_supp_arterial_sub.nii.gz
   bigimage 4 maxSize [512, 512, 470]
   Setting physical space of output average image based on largest image
   Averaging 2 images with dim = 3 vector components 1
   reading ./initialCOM1_0_VT_00026_vein_supp_arterial_sub.nii.gz
   reading ./initialCOM1_1_VT_00007_vein_supp_arterial_sub.nii.gz
   writing output
   Sharpening method none

---

Creating template antsBTPtemplate2.nii.gz from a population average image from the inputs.
/home/Reg_2/VT_00026_venous_pc.nii.gz /home/Reg_2/VT_00007_venous_pc.nii.gz

bigimage 4 maxSize [512, 512, 470]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading /home/Reg_2/VT_00026_venous_pc.nii.gz
reading /home/Reg_2/VT_00007_venous_pc.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: /home/Reg_2/VT_00026_venous_pc.nii.gz
Reference image: antsBTPtemplate2.nii.gz

The composite transform comprises the following transforms (in order):

1. ./initialCOM2_0_VT_00026_venous_pc.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM2_0_VT_00026_venous_pc.nii.gz
   Using double precision for computations.
   Input scalar image: /home/Reg_2/VT_00007_venous_pc.nii.gz
   Reference image: antsBTPtemplate2.nii.gz
   =============================================================================
   The composite transform comprises the following transforms (in order):
2. ./initialCOM2_1_VT_00007_venous_pc.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM2_1_VT_00007_venous_pc.nii.gz
   bigimage 4 maxSize [512, 512, 470]
   Setting physical space of output average image based on largest image
   Averaging 2 images with dim = 3 vector components 1
   reading ./initialCOM2_0_VT_00026_venous_pc.nii.gz
   reading ./initialCOM2_1_VT_00007_venous_pc.nii.gz
   writing output
   Sharpening method none

---

Creating template antsBTPtemplate3.nii.gz from a population average image from the inputs.
/home/Reg_2/VT_00026_artery_supp_venous_sub.nii.gz /home/Reg_2/VT_00007_artery_supp_venous_sub.nii.gz

bigimage 4 maxSize [512, 512, 470]
Setting physical space of output average image based on largest image
Averaging 2 images with dim = 3 vector components 1
reading /home/Reg_2/VT_00026_artery_supp_venous_sub.nii.gz
reading /home/Reg_2/VT_00007_artery_supp_venous_sub.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: /home/Reg_2/VT_00026_artery_supp_venous_sub.nii.gz
Reference image: antsBTPtemplate3.nii.gz

The composite transform comprises the following transforms (in order):

1. ./initialCOM3_0_VT_00026_artery_supp_venous_sub.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM3_0_VT_00026_artery_supp_venous_sub.nii.gz
   Using double precision for computations.
   Input scalar image: /home/Reg_2/VT_00007_artery_supp_venous_sub.nii.gz
   Reference image: antsBTPtemplate3.nii.gz
   =============================================================================
   The composite transform comprises the following transforms (in order):
2. ./initialCOM3_1_VT_00007_artery_supp_venous_sub.mat (type = TranslationTransform)
   =============================================================================
   Default pixel value: 0
   Interpolation type: LinearInterpolateImageFunction
   Output warped image: ./initialCOM3_1_VT_00007_artery_supp_venous_sub.nii.gz
   bigimage 4 maxSize [512, 512, 470]
   Setting physical space of output average image based on largest image
   Averaging 2 images with dim = 3 vector components 1
   reading ./initialCOM3_0_VT_00026_artery_supp_venous_sub.nii.gz
   reading ./initialCOM3_1_VT_00007_artery_supp_venous_sub.nii.gz
   writing output
   Sharpening method none

---

Start to build templates: antsBTPtemplate0.nii.gz antsBTPtemplate1.nii.gz antsBTPtemplate2.nii.gz antsBTPtemplate3.nii.gz

---

Mapping parameters

Dimensionality: 3
Do N4 bias correction: 0
Back up each iteration: 1
Similarity metric: MI MI MI MI
Gradient step: 0.2
Transformation: SyN
Max iterations: 100x100x70x20
Smoothing factors: 3x2x1x0
Shrink factors: 6x4x2x1
Output prefix: antsBTP
Template: antsBTPtemplate
Template update steps: 20
Template population: /home/subjectList_2.csv
Number of modalities: 4
Modality weights:
Image statistic: 0
Sharpening method: 1
Shape update full affine: 1

---

Starting ANTS registration on max 2 cpucores. Iteration: 1 of 20
Progress can be viewed in job*_0_metriclog.txt

Using max 2 parallel threads
Running sh ./job_00_r.sh
Running sh ./job_01_r.sh
Killed
Transform file does not exist: ./antsBTPVT_00026_arterial_pc00GenericAffine.mat
Transform file does not exist: ./antsBTPVT_00026_arterial_pc00GenericAffine.mat
Transform file does not exist: ./antsBTPVT_00026_arterial_pc00GenericAffine.mat
Transform file does not exist: ./antsBTPVT_00026_arterial_pc00GenericAffine.mat

Data to reproduce the problem

Sorry, I can't share data.
Here is the csv file
subjectList_2.csv

[ntustison]

Are you able to run one of these 2-D template building examples?

[cookpa]

The "Killed" message suggests the system is killing the processes for some reason.

Is this a PC or a compute cluster?

You might try running without pexec, ie use -c 0.