Operating system and version
Apptainer: docker://mathdugre/ants:flint-base
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
Manual compilation with commit 705a652ae14dffe774a561f4adffd9c395bcd7bb
ANTs installation type
Compiled from source
Summary of the problem
Current behavior
When using the --write-interval-volumes flag, files .nii.gz files are written to the current directory instead of the output directory.
Expected behavior
Files written to the specified output directory, along with the transform files.
Commands to reproduce the problem.
DATA_DIR=...
OUTPUT_DIR=...
SIF_IMG=...
FIXED_IMG=...
INPUT_IMG=...
apptainer exec --cleanenv \
-B ${DATA_DIR}:${DATA_DIR} \
-B ${OUTPUT_DIR}:${OUTPUT_DIR} \
${SIF_IMG} antsRegistration \
--verbose 1 \
--dimensionality 3 \
--collapse-output-transforms 0 \
--use-histogram-matching 0 \
--winsorize-image-intensities [0.005,0.995] \
--interpolation Linear \
--random-seed 1 \
--print-similarity-measure-interval 1 \
--write-interval-volumes 1 \
--output [${OUTPUT_DIR}/,${OUTPUT_DIR}/Warped.nii.gz,${OUTPUT_DIR}/InverseWarped.nii.gz] \
--initial-moving-transform [${FIXED_IMG},${INPUT_IMG},1] \
--transform Rigid[0.1] \
--metric MI[${FIXED_IMG},${INPUT_IMG},1,32,Regular,0.25] \
--convergence [1000x500x250x100,1e-6,10] \
--shrink-factors 8x4x2x1 \
--smoothing-sigmas 3x2x1x0vox
Output of the command with verbose output.
Files created in PWD directory:
find . -name "Stage*"
./Stage1_level1_Iter0004.nii.gz
./Stage1_level1_Iter0001.nii.gz
./Stage1_level1_Iter0002.nii.gz
./Stage1_level1_Iter0003.nii.gz
./Stage1_level1_Iter0005.nii.gz
Data to reproduce the problem
Any data
Operating system and version
Apptainer: docker://mathdugre/ants:flint-base
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
Manual compilation with commit
705a652ae14dffe774a561f4adffd9c395bcd7bbANTs installation type
Compiled from source
Summary of the problem
Current behavior
When using the --write-interval-volumes flag, files
.nii.gzfiles are written to the current directory instead of the output directory.Expected behavior
Files written to the specified output directory, along with the transform files.
Commands to reproduce the problem.
Output of the command with verbose output.
Files created in
PWDdirectory:Data to reproduce the problem
Any data