Pb Chimpanzee data application

[MaeligChauvel]

Command used : singularity run -e khanlab_hippunfold_1.5.1.sif TryChimpanzeedata OutputTestFolder participant --modality T1w --cores 20 --rigid-reg-template --skip-inject-template-labels

Error message :

Config file config/snakebids.yml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job stats:
job count

---

affine_gii_to_native 6
all 1
archive_work_after_final 1
calculate_curvature_from_surface1 2
calculate_curvature_from_surface2 2
calculate_gyrification1 2
calculate_gyrification2 2
calculate_surface_area1 2
calculate_surface_area2 2
calculate_thickness_from_surface1 2
calculate_thickness_from_surface2 2
combine_tissue_subfield_labels_corobl 2
compose_warps_native_to_unfold 2
compose_warps_unfold_to_crop_native 2
correct_nan_vertices1 6
correct_nan_vertices2 6
cp_unfolded_noconstrain 2
create_dscalar_metric_cifti 3
create_native_coord_ref 2
create_native_crop_ref 2
create_spec_file_hipp 2
create_warps_hipp 2
equivolume_coords 2
expand_unfolded_warps 4
get_subfield_vols_subj 1
label_subfields_from_vol_coords_corobl 2
laplace_coords_hipp 6
merge_lr_spec_file 1
metric_to_nii 6
normalize_curvature1 2
normalize_curvature2 2
plot_subj_subfields 1
qc_subfield 2
qc_subfield_surf 2
resample_coords_native_crop 8
resample_native_to_crop 2
resample_subfields_native_crop 2
resample_subfields_to_native 2
resample_unfoldreg_subfields 2
unfolded_registration 2
warp_gii_unfold2corobl1 6
warp_gii_unfold2corobl2 6
warp_gii_unfoldreg 6
total 122

Select jobs to execute...

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-L_laplace-hipp.txt
jobid: 24
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=PD, hemi=L
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-R_laplace-hipp.txt
jobid: 79
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=AP, hemi=R
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_laplace-hipp.txt
jobid: 149
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=IO, hemi=L
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule equivolume_coords:
input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt
jobid: 83
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz
wildcards: subject=Jimmy, dir=IO, hemi=R
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_laplace-hipp.txt
jobid: 151
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=IO, hemi=R
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule equivolume_coords:
input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt
jobid: 25
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz
wildcards: subject=Jimmy, dir=IO, hemi=L
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-L_laplace-hipp.txt
jobid: 12
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=AP, hemi=L
resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025]
rule laplace_coords_hipp:
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-R_laplace-hipp.txt
jobid: 82
reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
wildcards: subject=Jimmy, dir=PD, hemi=R
resources: tmpdir=/tmp, time=30

/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0
warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
Traceback (most recent call last):
Traceback (most recent call last):
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpbi7_agqc.laplace_coords.py", line 8, in
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp8gp7sng2.laplace_coords.py", line 8, in
Traceback (most recent call last):
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpwlqp024h.laplace_coords.py", line 8, in
from astropy.convolution import convolve as nan_convolve
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
Traceback (most recent call last):
from astropy.convolution import convolve as nan_convolve
from astropy.convolution import convolve as nan_convolve
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmprm5jlijt.laplace_coords.py", line 8, in
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
from astropy.convolution import convolve as nan_convolve
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from .utils import (discretize_model, add_kernel_arrays_1D,
from .utils import (discretize_model, add_kernel_arrays_1D,
from .utils import (discretize_model, add_kernel_arrays_1D,
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
from .utils import (discretize_model, add_kernel_arrays_1D,
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
Traceback (most recent call last):
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp6i9ei5j7.laplace_coords.py", line 8, in
from astropy.convolution import convolve as nan_convolve
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from astropy.modeling.core import FittableModel, custom_model
from astropy.modeling.core import FittableModel, custom_model
from astropy.modeling.core import FittableModel, custom_model
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
from .utils import (discretize_model, add_kernel_arrays_1D,
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
from astropy.modeling.core import FittableModel, custom_model
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
from astropy.modeling.core import FittableModel, custom_model
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
from . import fitting
from . import fitting
from . import fitting
from . import fitting
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
from . import fitting
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
Traceback (most recent call last):
File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmph24aoyid.laplace_coords.py", line 8, in
from astropy.units import Quantity
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
from astropy.units import Quantity
from astropy.units import Quantity
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
from astropy.units import Quantity
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
from astropy.units import Quantity
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
from astropy.convolution import convolve as nan_convolve
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in
from .core import * # noqa
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in
from .utils import (discretize_model, add_kernel_arrays_1D,
File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in
from astropy.modeling.core import FittableModel, custom_model
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in
from . import fitting
File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in
from .quantity import *
from .quantity import *
from .quantity import *
from .quantity import *
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
from astropy.units import Quantity
File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in
from .quantity import *
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
from .quantity import *
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit,
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in
from . import helpers, function_helpers
from . import helpers, function_helpers
from . import helpers, function_helpers
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
from . import helpers, function_helpers
from . import helpers, function_helpers
from . import helpers, function_helpers
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in
np.asscalar,
np.asscalar,
np.asscalar,
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
np.asscalar,
np.asscalar,
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
np.asscalar,
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'asscalar'
[Tue Mar 18 15:48:38 2025]
Error in rule laplace_coords_hipp:
jobid: 149
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_laplace-hipp.txt (check log file(s) for error details)

[Tue Mar 18 15:48:38 2025]
[Tue Mar 18 15:48:38 2025]
Error in rule laplace_coords_hipp:
jobid: 151
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_laplace-hipp.txt (check log file(s) for error details)

Error in rule laplace_coords_hipp:
jobid: 24
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-L_laplace-hipp.txt (check log file(s) for error details)

[Tue Mar 18 15:48:38 2025]
Error in rule laplace_coords_hipp:
jobid: 79
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-R_laplace-hipp.txt (check log file(s) for error details)

RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpwlqp024h.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpbi7_agqc.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp8gp7sng2.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
[Tue Mar 18 15:48:38 2025]
Error in rule laplace_coords_hipp:
jobid: 12
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-L_laplace-hipp.txt (check log file(s) for error details)

RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp6i9ei5j7.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmph24aoyid.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
[Tue Mar 18 15:48:38 2025]
Error in rule laplace_coords_hipp:
jobid: 82
input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-R_laplace-hipp.txt (check log file(s) for error details)

RuleException:
CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84:
Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmprm5jlijt.laplace_coords.py' returned non-zero exit status 1.
File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp
File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
[Tue Mar 18 15:48:44 2025]
Error in rule equivolume_coords:
jobid: 83
input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt (check log file(s) for error details)
shell:
python /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/scripts/equivolume_coords.py /tmp work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz &> logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Mar 18 15:48:44 2025]
Error in rule equivolume_coords:
jobid: 25
input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz
output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz
log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt (check log file(s) for error details)
shell:
python /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/scripts/equivolume_coords.py /tmp work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz &> logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-03-18T154835.359670.snakemake.log

[jordandekraker]

another quick note from our conversation today:
we tried with & without template shape injection, the error is the same. There are likely two issues:

1. the segmentation is not correct because we are using chimpanzee data here with a human (and also tried marmoset) nnunet/registration. But I dont think this would throw an error, just give bad results.
2. this specific error message seems to be caused by an issue with astropy. I wonder if we've accidentally broken our dependencies somewhere...

[akhanf]

No, it looks like like the problem is stemming from the local python environment getting picked up and having conflicts:

File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr

My recommendation is to remove any python packages from your ~/.local/lib path (it is not recommended to put things there directly anyways).. you might be able to work around by altering your singularity bind paths too, but I would just suggest clearing it out (and using something like virtualenv, pipx or uvx for those things you had installed there..)

[jordandekraker]

Yes it sounds like that should work, but I'm surprised that singularity includes ~/.local/lib in its path, since the singularity -e flag is being used. This makes me worry that singularity might not be quite as isolating as I'd hoped. I wonder if there's something we can include in the Dockerfile to avoid this issue?

[akhanf]

Recall that the -e flag only clears the environment variables, ie it doesn't control what is on your filesystem. If python sees ~/.local/lib/ it tries to look for packages there..

[akhanf]

Ie it is not coming from the environment variables but from the files on the filesystem

[jordandekraker]

Seems like a quick fix would be to add PYTHONNOUSERSITE to the Dockerfile
https://stackoverflow.com/questions/41360022/how-to-ignore-python-module-in-local-lib-python2-7-site-packages

[akhanf]

ah didn't know about that env var -- yes can be set in the dockerfile -- note you would also have to set SINGULARITYENV_PYTHONNOUSERSITE (and for future-proofing maybe: APPTAINERENV_PYTHONNOUSERSITE) (nevermind that would only be for --use-singularity cases..)

[akhanf]

just looping back so we can close this if possible -- did this correct the issue @MaeligChauvel ?

[MaeligChauvel]

Hi, I need to check what I can do on my side, please don't close it for now. Best regards, Maelig

…

________________________________ De : Ali Khan ***@***.***> Envoyé : jeudi 17 avril 2025 14:30 À : khanlab/hippunfold ***@***.***> Cc : Maelig Chauvel ***@***.***>; Mention ***@***.***> Objet : Re: [khanlab/hippunfold] Pb Chimpanzee data application (Issue #400) just looping back so we can close this if possible -- did this correct the issue @MaeligChauvel<https://github.com/MaeligChauvel> ? — Reply to this email directly, view it on GitHub<#400 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BI65DFMPAHUR4QTOBJ6RBTD2Z63J7AVCNFSM6AAAAABZIMF23OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMJTGEZTGNZWGE>. You are receiving this because you were mentioned.Message ID: ***@***.***> [https://avatars.githubusercontent.com/u/11492701?s=20&v=4]akhanf left a comment (khanlab/hippunfold#400)<#400 (comment)> just looping back so we can close this if possible -- did this correct the issue @MaeligChauvel<https://github.com/MaeligChauvel> ? — Reply to this email directly, view it on GitHub<#400 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BI65DFMPAHUR4QTOBJ6RBTD2Z63J7AVCNFSM6AAAAABZIMF23OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMJTGEZTGNZWGE>. You are receiving this because you were mentioned.Message ID: ***@***.***>