I ran into this error in the PostFreeSurfer stage that in searching looks like it may be related to an issue with ANTs known as the "bracket expansion bug": https://github.com/ANTsX/ANTs/issues/712
What command did you use?
Routine Docker execution in PostFreeSurfer stage.
What version of the abcd-hcp pipeline are you using?
v0.1.0
Directory Structure
No response
Relevant log output
Truncated relevant portion from the 'AtlasRegistration to MNI152' section on calling /opt/ants/antsRegistrationSyN.sh
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PixelContainer:
ImportImageContainer (0x4613b20)
RTTI typeinfo: itk::ImportImageContainer<unsigned long, double>
Reference Count: 1
Modified Time: 3052
Debug: Off
Object Name:
Observers:
none
Pointer: 0x7f23dff9a010
Container manages memory: true
Size: 7221032
Capacity: 7221032
Weighting = 1
Sampling strategy = none
Number of bins = 32
Radius = 4
Sampling percentage = 1
Transform = SyN
Gradient step = 0.1
Update field sigma (voxel space) = 3
Total field sigma (voxel space) = 0
Update field time sigma = 0
Total field time sigma = 0
Number of time indices = 0
Number of time point samples = 0
Registration using 3 total stages.
Stage 0
iterations = 2
convergence threshold = 1e-06
convergence window size = 10
number of levels = 1
using the Mattes MI metric (number of bins = 32, weight = 1)
preprocessing: winsorizing the image intensities
ERROR: The number of shrink factors does not match the number of levels.
Shrink Factors: 4
Number Of Levels: 1
antsApplyTransform
Add any additional information or context about the problem here.
I was able to work around by adding 'set -f' in the ansRegistrationSyN.sh script within the Docker container with the following command:
docker run -it --entrypoint=/bin/bash -v /data/bids:/bids_input -v /data/bids/derivatives/abcd-hcp-pipeline:/output -v /freesurfer-license.txt:/license.txt dcanumn/abcd-hcp-pipeline:v0.1.0 -c 'sed -i "2i set -f" /opt/ants/antsRegistrationSyN.sh; /entrypoint.sh /bids_input /output --freesurfer-license=/license.txt --ncpus 12 --participant-label 123 --session-id 01 --stage PostFreeSurfer:PostFreeSurfer'
You may want to consider updating the ANTs version in the Docker container.
What happened?
I ran into this error in the PostFreeSurfer stage that in searching looks like it may be related to an issue with ANTs known as the "bracket expansion bug": https://github.com/ANTsX/ANTs/issues/712
What command did you use?
What version of the abcd-hcp pipeline are you using?
v0.1.0
Directory Structure
No response
Relevant log output
Add any additional information or context about the problem here.
I was able to work around by adding 'set -f' in the ansRegistrationSyN.sh script within the Docker container with the following command:
docker run -it --entrypoint=/bin/bash -v /data/bids:/bids_input -v /data/bids/derivatives/abcd-hcp-pipeline:/output -v /freesurfer-license.txt:/license.txt dcanumn/abcd-hcp-pipeline:v0.1.0 -c 'sed -i "2i set -f" /opt/ants/antsRegistrationSyN.sh; /entrypoint.sh /bids_input /output --freesurfer-license=/license.txt --ncpus 12 --participant-label 123 --session-id 01 --stage PostFreeSurfer:PostFreeSurfer'
You may want to consider updating the ANTs version in the Docker container.