COMMIT2: mismatch between params_IC and input tractogram #154
Description
Description
I am following the COMMIT2 tutorial and trying to apply it to the tractoInferno dataset, for which I have obtain tractograms. I can successfully run COMMIT, but when I switch to COMMIT2, the following command fails:
# Set the regularisation
mit.set_regularisation(
regularisers=('group_lasso', None, None),
is_nonnegative=(True, True, True),
lambdas=(perc_lambda, None, None),
params=(params_IC, None, None)
)
The error occurs because params_IC has shape (718626,) while the original tractogram (input_fibers_connecting.tck) has shape (719560,).
File "/home/simona/work/code/Default/Ontheside/./COMMIT.py", line 185, in process_data
mit.set_regularisation(
~~~~~~~~~~~~~~~~~~~~~~^
regularisers = ('group_lasso', None, None),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...<2 lines>...
params = (params_IC, None, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "commit/core.pyx", line 1118, in commit.core.Evaluation.set_regularisation
ValueError: operands could not be broadcast together with shapes (719560,) (718626,)
Details
The issue seems to be related to the trk2dictionary.run() step:
trk2dictionary.run(
filename_tractogram='input_fibers_connecting.tck',
TCK_ref_image=args.dwi_nii,
min_seg_len=0.0000001,
verbose=4
# min_seg_len = 0.0,
# blur_clust_thr = 0,
# # filename_mask = args.wm_nii, really changes the number of streamlines in IC compartments
# fiber_shift=0.5
)
When creating IC compartments, not all streamlines are considered. Here is the relevant log excerpt:
Creating data structure from tractogram
* Configuration:
- Segment position = COMPUTE INTERSECTIONS
- Coordinates shift in X = 0.000 (voxel-size units)
- Coordinates shift in Y = 0.000 (voxel-size units)
- Coordinates shift in Z = 0.000 (voxel-size units)
- Min segment len = 1.00e-07 mm
- Min streamline len = 0.00 mm
- Max streamline len = 250.00 mm
- Do not blur streamlines
- Output written to "./COMMIT"
- Temporary files written to "./COMMIT/temp"
- Using parallel computation with 22 threads
* Loading data:
- Tractogram:
- geometry taken from "sub-1006__dwi.nii.gz"
- 142 x 174 x 120
- 1.000 x 1.000 x 1.000
- 719560 streamlines
- No mask specified to restrict IC compartments
- No dataset specified for EC compartments
- No mask specified to restrict ISO compartments
* Exporting IC compartments:
[ 718626 streamlines kept, 76441230 segments in total ]
* Exporting EC compartments:
[ 0 voxels, 0 segments ]
* Exporting ISO compartments:
[ 1343370 voxels ]
* Saving data structure in "./COMMIT"
* Saving TDI and MASK maps
I tried changing many trk2dictionary parameters to reduce the mismatch between the shapes, but I cannot eliminate it completely.
Question
- How can I ensure that
params_ICmatches the original tractogram? - Is there a way to export the streamlines from IC components?
- Alternatively, how can I make
input_fibers_connecting.tckidentical to the IC components from the start? - If necessary, I am willing to manually create the dictionary. Can you describe how that should look like?
Any advice would be greatly appreciated!