usage: __main__.py [-h]
[--tractogram_clustering_thr TRACTOGRAM_CLUSTERING_THR]
[--model_clustering_thr MODEL_CLUSTERING_THR]
[--pruning_thr PRUNING_THR] [--slr_threads SLR_THREADS]
[--seed SEED] [--inverse] [--no_empty]
[--in_pickle IN_PICKLE | --out_pickle OUT_PICKLE]
[--in_tractogram_ref IN_TRACTOGRAM_REF]
[--in_model_ref IN_MODEL_REF]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_tractogram in_model in_transfo out_tractogram
Segment a single bundle by computing a simple Recobundles (single-atlas &
single-parameters).
For multiple bundles segmentation (using RecobundlesX / BundleSeg), see instead
>>> scil_tractogram_segment_with_bundleseg
Hints:
- The model needs to be cleaned and lightweight.
- The transform should come from ANTs: (using the --inverse flag)
>>> AntsRegistrationSyNQuick.sh -d 3 -m MODEL_REF -f SUBJ_REF
If you are unsure about the transformation 'direction', try with and without
the --inverse flag. If you are not using the right transformation 'direction'
a warning will pop up. If there is no warning in both cases, it means the
transformation is very close to identity and both 'directions' will work.
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Reference:
[1] Garyfallidis, E., Cote, M. A., Rheault, F., ... & Descoteaux, M. (2018).
Recognition of white matter bundles using local and global streamline-based
registration and clustering. NeuroImage, 170, 283-295.
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positional arguments:
in_tractogram Input tractogram filename.
in_model Model bundle to use for recognition. (Ex, a .trk file.
in_transfo Path for the transformation to model space (.txt, .npy or .mat).
out_tractogram Output tractogram filename.
options:
-h, --help show this help message and exit
--seed SEED Random number generator seed [None].
--inverse Use the inverse transformation.
--no_empty Do not write file if there is no streamline.
--in_pickle IN_PICKLE
Input pickle clusters map file.
Will override the tractogram_clustering_thr parameter.
--out_pickle OUT_PICKLE
Output pickle clusters map file.
--in_tractogram_ref IN_TRACTOGRAM_REF
Reference anatomy for in_tractogram (if tck/vtk/fib/dpy) file
support (.nii or .nii.gz).
--in_model_ref IN_MODEL_REF
Reference anatomy for in_model (if tck/vtk/fib/dpy) file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Recobundles options:
--tractogram_clustering_thr TRACTOGRAM_CLUSTERING_THR
Clustering threshold used for the whole brain. Default: 8.
--model_clustering_thr MODEL_CLUSTERING_THR
Clustering threshold used for the model [4mm].
--pruning_thr PRUNING_THR
MDF threshold used for final streamlines selection [6mm].
--slr_threads SLR_THREADS
Number of threads for SLR [1].
2.2.2