Tractometry_flow fails if not enough streamlines

[arnaudbore]

scil_compute_bundle_voxel_label_map.py

  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  Traceback (most recent call last):
    File "/usr/local/bin/scil_compute_bundle_voxel_label_map.py", line 33, in <module>
      sys.exit(load_entry_point('scilpy', 'console_scripts', 'scil_compute_bundle_voxel_label_map.py')())
    File "/scilpy/scripts/scil_compute_bundle_voxel_label_map.py", line 212, in main
      kd_tree = cKDTree(final_streamlines._data)
    File "_ckdtree.pyx", line 560, in scipy.spatial._ckdtree.cKDTree.__init__
  ValueError: data must be 2 dimensions

[yizhwan]

May I ask if there is a solution to this issue yet? I am receiving the same error when running tractometry_flow:
Error executing process > 'Bundle_Label_And_Distance_Maps (S17 - [:])'

Caused by:
Process Bundle_Label_And_Distance_Maps (S17 - [:]) terminated with an error exit status (1)

Command executed:

for bundle in S17__AC_ic.trk S17__AF_L_ic.trk S17__AF_R_ic.trk S17__CC_Fr_1_ic.trk S17__CC_Fr_2_ic.trk S17__CC_Oc_ic.trk S17__CC_Pa_ic.trk S17__CC_Pr_Po_ic.trk S17__CG_L_Po_ic.trk S17__CG_L_curve_ic.trk S17__CG_L_ic.trk S17__CG_R_Po_ic.trk S17__CG_R_ic.trk S17__FAT_L_ic.trk S17__FAT_R_ic.trk S17__FPT_L_Brainstem_ic.trk S17__FPT_L_ic.trk S17__FPT_R_ic.trk S17__ICP_L_ic.trk S17__IFOF_L_ic.trk S17__IFOF_R_ic.trk S17__ILF_L_ic.trk S17__ILF_R_ic.trk S17__MCP_ic.trk S17__MdLF_L_ic.trk S17__MdLF_R_ic.trk S17__OR_ML_L_ic.trk S17__OR_ML_R_ic.trk S17__POPT_L_Brainstem_ic.trk S17__POPT_L_ic.trk S17__POPT_R_Brainstem_ic.trk S17__POPT_R_ic.trk S17__PYT_L_Brainstem_ic.trk S17__PYT_L_ic.trk S17__PYT_R_Brainstem_ic.trk S17__PYT_R_ic.trk S17__SCP_L_ic.trk S17__SCP_R_ic.trk S17__SLF_L_ic.trk S17__SLF_R_ic.trk S17__UF_L_ic.trk S17__UF_R_ic.trk;
do if [[ $bundle == "__" ]]; then
pos=$(($(echo $bundle | grep -b -o __ | cut -d: -f1)+2))
bname=${bundle:$pos}
bname=$(basename $bname .trk)
else
bname=$(basename $bundle .trk)
fi
bname=${bname/_ic/}

  centroid=S17__${bname}_centroid_50.trk
  if [[ -f ${centroid} ]]; then
      scil_compute_bundle_voxel_label_map.py $bundle ${centroid} tmp_out -f

      mv tmp_out/labels_map.nii.gz S17__${bname}_labels.nii.gz
      mv tmp_out/distance_map.nii.gz S17__${bname}_distances.nii.gz

      mv tmp_out/labels.trk S17__${bname}_labels.trk
      mv tmp_out/distance.trk S17__${bname}_distances.trk
  fi

done

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File "/usr/local/bin/scil_compute_bundle_voxel_label_map.py", line 33, in
sys.exit(load_entry_point('scilpy', 'console_scripts', 'scil_compute_bundle_voxel_label_map.py')())
File "/scilpy/scripts/scil_compute_bundle_voxel_label_map.py", line 212, in main
kd_tree = cKDTree(final_streamlines._data)
File "_ckdtree.pyx", line 560, in scipy.spatial._ckdtree.cKDTree.init
ValueError: data must be 2 dimensions

Work dir:

/tract_flow/work/68/cd58748452dccb9c386f18767a2238

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line