Hi, tractoflow is running into an error when calculating the FRF and DTI metrics. Below is the command line along with the .command.err logs from both processes.
nextflow run /path/to/main.nf --input /path/to/data/ -with-singularity /path/to/scilus_1.5.0.sif -profile fully_reproducible -resume -with-report report.html --run_pft_tracking false --run_local_tracking true --local_seeding_mask_type fa --local_fa_seeding_mask_threshold 0.1 --local_tracking_mask_type fa --local_fa_tracking_mask_threshold 0.1
DTI_Metrics .command.err:
/work/86/f93c47147f953d97aacdeb3f776a03/.comand.err
Matplotlib created a temporary config/cache directory at /tmpdata/matplotlib-i8ca0s7s because the default path (/path/to/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
/usr/local/lib/python3.10/dist-packages/dipy/reconst/dti.py:498: RuntimeWarning: invalid value encountered in divide
return 3 * np.sqrt(6) * determinant((A_squiggle / A_s_norm))
Traceback (most recent call last):
File "/usr/local/bin/scil_compute_dti_metrics.py", line 33, in <module>
sys.exit(load_entry_point('scilpy', 'console_scripts', 'scil_compute_dti_metrics.py')())
File "/scilpy/scripts/scil_compute_dti_metrics.py", line 321, in main
pis_mask = np.max(S0 < DWI, axis=-1)
File "<__array_function__ internals>", line 180, in amax
File "/usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py", line 2793, in amax
return _wrapreduction(a, np.maximum, 'max', axis, None, out,
File "/usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity
compute_FRF .command.err:
/work/d9/898ca05b3092d00a1f0ab2f92c3d11/.comand.err
Matplotlib created a temporary config/cache directory at /tmpdata/matplotlib-5zlpzs6t because the default path (/path/to/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
WARNING:root:No white matter mask specified! Only mask will be used (if it has been supplied).
Be *VERY* careful about the estimation of the fiber response function to ensure no invalid voxel was used.
Traceback (most recent call last):
File "/usr/local/bin/scil_compute_ssst_frf.py", line 33, in <module>
sys.exit(load_entry_point('scilpy', 'console_scripts', 'scil_compute_ssst_frf.py')())
File "/scilpy/scripts/scil_compute_ssst_frf.py", line 117, in main
full_response = compute_ssst_frf(
File "/scilpy/scilpy/reconst/frf.py", line 116, in compute_ssst_frf
raise ValueError(
ValueError: Could not find at least 300 voxels with sufficient FA to estimate the FRF!
Not sure how to proceed.