conforming adding header info
Opened this issue · 1 comments
Description
When conforming happens from inside run_prediction it adds incorrect "TR" information to the image header.
Steps to Reproduce
Run run_prediction with an already conform input, e.g. from oasis and compare the conformed output image.
mri_info will show on the original:
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
and on the conformed:
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
So acquisition parameters change, while the image is identical (no conforming necessary as it is already).
Expected Behavior
Copy those values from the original header.
Environment
- FastSurfer Version: dev
- OS: macos
absl-py==2.1.0
certifi==2024.8.30
charset-normalizer==3.3.2
click==8.1.7
contourpy==1.3.0
cycler==0.12.1
Deprecated==1.2.14
filelock==3.16.0
fonttools==4.53.1
fsspec==2024.9.0
grpcio==1.66.1
h5py==3.11.0
humanize==4.10.0
idna==3.8
imageio==2.35.1
Jinja2==3.1.4
joblib==1.4.2
kiwisolver==1.4.7
lapy==1.1.1
lazy_loader==0.4
Markdown==3.7
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.9.2
mdurl==0.1.2
mpmath==1.3.0
networkx==3.3
nibabel==5.2.1
numpy==1.26.4
packaging==24.1
pandas==2.2.2
pillow==10.4.0
plotly==5.24.0
protobuf==5.28.0
psutil==6.0.0
Pygments==2.18.0
pyparsing==3.1.4
python-dateutil==2.9.0.post0
pytz==2024.1
PyYAML==6.0.2
requests==2.32.3
rich==13.8.0
scikit-image==0.24.0
scikit-learn==1.5.1
scipy==1.14.1
shellingham==1.5.4
SimpleITK==2.4.0
six==1.16.0
sympy==1.13.2
tenacity==9.0.0
tensorboard==2.17.1
tensorboard-data-server==0.7.2
threadpoolctl==3.5.0
tifffile==2024.8.30
torch==2.4.1
torchio==0.19.9
torchvision==0.19.1
tqdm==4.66.5
typer==0.12.5
typing_extensions==4.12.2
tzdata==2024.1
urllib3==2.2.2
Werkzeug==3.0.4
wrapt==1.16.0
yacs==0.1.8
Execution
python3.10 FastSurfer/FastSurferCNN/run_prediction.py --t1 /....../T1_input.nii.gz --asegdkt_segfile /...../aparc+aseg.orig.nii.gz --conformed_name /...../T1_conform.nii.gz --brainmask_name /...../mask.nii.gz --aseg_name /...../aseg.auto_noCCseg.nii.gz --sid OAS1_0111_MR2_l --seg_log /dev/null --vox_size min --batch_size 1 --viewagg_device auto --device mps