Can't open the last modality with antsMultivariateTemplateConstruction2.sh
Ludwig-T opened this issue · comments
Operating system and version
Ubuntu 22.04.3 LTS
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
v2.3.5.post101-g1c5ae7c
ANTs installation type
Other (please specify below)
Summary of the problem
I am constructing a template with antsMultivariateTemplateConstruction2.sh using three modalities. It can't open the last (third) modality. I have tried swaping the order of the modalities and using the first modality as the third modality as well. I have tried refering to the files with relative and absolute path. Therefore I don't think it is a problem with the files. As the log correctly outputs the file paths I do not think there is a problem with the input .csv file
Ants is install from:
https://github.com/cookpa/antsInstallExample
Commands to reproduce the problem.
antsMultivariateTemplateConstruction2.sh -d 3 -w 1x1x1 -k 3 -i 5 -g 0.2 -j 8 -c 2 -f 6x4x2x1 -s 3x2x1x0 -q 501x251x151x76 -n 0 -r 1 -l 1 -m MI -t BSplineSyN -y 1 -v 8gb -p /root/dir/templates/templateception/ver-0/ver-0_/ -o /root/dir/templates/templateception/ver-0/ver-0_ /root/dir/templates/templateception/template_paths.csv
Output of the command with verbose output.
Multivariate template construction using the following 3-tuples:
templates/final_templates/ver-3/age-15/age-15_ver-3_template_aseg.nii.gz templates/final_templates/ver-3/age-15/age-15_ver-3_template1.nii.gz templates/final_templates/ver-3/age-15/age-15_ver-3_template0.nii.gz
templates/final_templates/ver-3/age-16/age-16_ver-3_template_aseg.nii.gz templates/final_templates/ver-3/age-16/age-16_ver-3_template1.nii.gz templates/final_templates/ver-3/age-16/age-16_ver-3_template0.nii.gz
templates/final_templates/ver-3/age-17/age-17_ver-3_template_aseg.nii.gz templates/final_templates/ver-3/age-17/age-17_ver-3_template1.nii.gz templates/final_templates/ver-3/age-17/age-17_ver-3_template0.nii.gz
Creating template /root/dir/templates/templateception/ver-0/ver-0_template0.nii.gz from a population average image from the inputs.
templates/final_templates/ver-3/age-15/age-15_ver-3_template_aseg.nii.gz templates/final_templates/ver-3/age-16/age-16_ver-3_template_aseg.nii.gz templates/final_templates/ver-3/age-17/age-17_ver-3_template_aseg.nii.gz
bigimage 4 maxSize [140, 140, 92]
Setting physical space of output average image based on largest image
Averaging 3 images with dim = 3 vector components 1
reading templates/final_templates/ver-3/age-15/age-15_ver-3_template_aseg.nii.gz
reading templates/final_templates/ver-3/age-16/age-16_ver-3_template_aseg.nii.gz
reading templates/final_templates/ver-3/age-17/age-17_ver-3_template_aseg.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-15/age-15_ver-3_template_aseg.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template0.nii.gz
The composite transform comprises the following transforms (in order):
- /root/dir/templates/templateception/ver-0/initialCOM0_0_age-15_ver-3_template_aseg.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM0_0_age-15_ver-3_template_aseg.nii.gz
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-16/age-16_ver-3_template_aseg.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template0.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): - /root/dir/templates/templateception/ver-0/initialCOM0_1_age-16_ver-3_template_aseg.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM0_1_age-16_ver-3_template_aseg.nii.gz
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-17/age-17_ver-3_template_aseg.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template0.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): - /root/dir/templates/templateception/ver-0/initialCOM0_2_age-17_ver-3_template_aseg.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM0_2_age-17_ver-3_template_aseg.nii.gz
bigimage 4 maxSize [140, 140, 92]
Setting physical space of output average image based on largest image
Averaging 3 images with dim = 3 vector components 1
reading /root/dir/templates/templateception/ver-0/initialCOM0_0_age-15_ver-3_template_aseg.nii.gz
reading /root/dir/templates/templateception/ver-0/initialCOM0_1_age-16_ver-3_template_aseg.nii.gz
reading /root/dir/templates/templateception/ver-0/initialCOM0_2_age-17_ver-3_template_aseg.nii.gz
writing output
Sharpening method none
Creating template /root/dir/templates/templateception/ver-0/ver-0_template1.nii.gz from a population average image from the inputs.
templates/final_templates/ver-3/age-15/age-15_ver-3_template1.nii.gz templates/final_templates/ver-3/age-16/age-16_ver-3_template1.nii.gz templates/final_templates/ver-3/age-17/age-17_ver-3_template1.nii.gz
bigimage 4 maxSize [140, 140, 92]
Setting physical space of output average image based on largest image
Averaging 3 images with dim = 3 vector components 1
reading templates/final_templates/ver-3/age-15/age-15_ver-3_template1.nii.gz
reading templates/final_templates/ver-3/age-16/age-16_ver-3_template1.nii.gz
reading templates/final_templates/ver-3/age-17/age-17_ver-3_template1.nii.gz
writing output
Sharpening method none
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-15/age-15_ver-3_template1.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template1.nii.gz
The composite transform comprises the following transforms (in order):
- /root/dir/templates/templateception/ver-0/initialCOM1_0_age-15_ver-3_template1.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM1_0_age-15_ver-3_template1.nii.gz
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-16/age-16_ver-3_template1.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template1.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): - /root/dir/templates/templateception/ver-0/initialCOM1_1_age-16_ver-3_template1.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM1_1_age-16_ver-3_template1.nii.gz
Using double precision for computations.
Input scalar image: templates/final_templates/ver-3/age-17/age-17_ver-3_template1.nii.gz
Reference image: /root/dir/templates/templateception/ver-0/ver-0_template1.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): - /root/dir/templates/templateception/ver-0/initialCOM1_2_age-17_ver-3_template1.mat (type = TranslationTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /root/dir/templates/templateception/ver-0/initialCOM1_2_age-17_ver-3_template1.nii.gz
bigimage 4 maxSize [140, 140, 92]
Setting physical space of output average image based on largest image
Averaging 3 images with dim = 3 vector components 1
reading /root/dir/templates/templateception/ver-0/initialCOM1_0_age-15_ver-3_template1.nii.gz
reading /root/dir/templates/templateception/ver-0/initialCOM1_1_age-16_ver-3_template1.nii.gz
reading /root/dir/templates/templateception/ver-0/initialCOM1_2_age-17_ver-3_template1.nii.gz
writing output
Sharpening method none
Creating template /root/dir/templates/templateception/ver-0/ver-0_template2.nii.gz from a population average image from the inputs.
templates/final_templates/ver-3/age-15/age-15_ver-3_template0.nii.gz
templates/final_templates/ver-3/age-16/age-16_ver-3_template0.nii.gz
templates/final_templates/ver-3/age-17/age-17_ver-3_template0.nii.gz
Cannot read input file: templates/final_templates/ver-3/age-15/age-15_ver-3_template0.nii.gz
summarizeimageset: ERROR - output file /root/dir/templates/templateception/ver-0/ver-0_template2.nii.gz could not be created
antsMultivariateTemplateConstruction2.sh -d 3 -w 1x1x1 -k 3 -i 5 -g 0.2 -j 8 -c 2 -f 6x4x2x1 -s 3x2x1x0 -q 501x251x151x76 -n 0 -r 1 -l 1 -m MI -t BSplineSyN -y 1 -v 8gb -p /root/dir/templates/templateception/ver-0/ver-0_/ -o /root/dir/templates/templateception/ver-0/ver-0_ /root/dir/templates/templateception/template_paths.csv
Data to reproduce the problem
I cannot share the data.
Probably the same issue as #1745. I'm investigating
Can you try
cat -A template_paths.csv
If you see ^M then the problem is the carriage return. Fix with
perl -i -pe 's/\r//g' template_paths.csv
This appears to have fixed it. Thanks for the quick replies!