Error with conda example on fresh install on macOS

[Ian-Goodall-Halliwell]

Why trying to run the conda example in the dev-v2.0.0 docs, I get hit with the following errors:

/bin/bash: wb_command: command not found
/bin/bash: c3d: command not found
/bin/bash: N4BiasFieldCorrection: command not found

Is the user supposed to download and add these (Connectome Workbench, Convert3D, ANTs) to their path?
I can add more environment details if it's helpful.

Full log below:

`(hippunfold-env) ian@Ians-MacBook-Air hippunfold % hippunfold ds002168 ds002168_hippunfold participant --modality T1w --cores all

Assuming unrestricted shared filesystem usage.
host: Mac.ht.home
Building DAG of jobs...
CyclicGraphException in rule native_metric_to_unfold_nii in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/native_surf.smk", line 1068:
Cyclic dependency on rule native_metric_to_unfold_nii.

CyclicGraphException in rule native_metric_to_unfold_nii in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/native_surf.smk", line 1068:
Cyclic dependency on rule native_metric_to_unfold_nii.

Using shell: /bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job stats:
job count

---

affine_gii_to_native 4
all 1
atlas_metric_to_unfold_nii 6
calculate_curvature 4
calculate_legacy_gyrification 4
calculate_surface_area 8
calculate_thickness 4
combine_tissue_subfield_labels_corobl 2
compose_template_xfm_corobl 1
compute_halfthick_mask 8
convert_inout_warp_from_itk_to_world 8
convert_template_xfm_ras2itk 1
convert_unfoldreg_warp_from_itk_to_world 2
cp_native_surf_to_root 22
cp_surf_to_root 6
cp_template_to_unfold 4
create_dlabel_cifti_subfields 1
create_dlabel_cifti_subfields_native 1
create_dscalar_metric_cifti 6
create_dscalar_metric_cifti_native 6
create_native_crop_ref 2
create_spec_file_dentate 2
create_spec_file_dentate_native 2
create_spec_file_hipp 2
create_spec_file_hipp_native 2
create_unfold_ref 1
create_upsampled_coords_ref 4
download_extract_atlas 1
download_extract_template 2
download_nnunet_model 1
extend_warp_2d_to_3d 2
extract_unfold_ref_slice 2
gen_native_mesh 4
get_boundary_vertices 4
get_label_mask 4
get_nan_mask 4
get_src_sink_mask 24
get_src_sink_sdt 16
get_subfield_vols_subj 1
import_template_dseg 2
import_template_dseg_dentate 2
label_subfields_from_vol_coords_corobl 2
laplace_beltrami 8
laynii_layers_equidist 4
map_src_sink_sdt_to_surf 16
merge_hipp_dentate_spec_file 1
merge_hipp_dentate_spec_file_native 1
merge_lr_spec_file 2
merge_lr_spec_file_native 2
n4_t1 1
native_metric_to_unfold_nii 6
pad_unfold_ref 2
plot_subj_subfields 1
postproc_boundary_vertices 4
prep_dseg_for_laynii 4
prep_segs_for_greedy 4
qc_nnunet_dice 2
qc_nnunet_f3d 2
qc_reg_to_template 1
qc_subfield 2
qc_subfield_surf 4
reg_to_template 1
register_midthickness 8
reinsert_subject_labels 4
resample_atlas_subfields_to_native_surf 2
resample_atlas_subfields_to_std_density 2
resample_native_metric_to_std_density 12
resample_native_surf_to_std_density 6
resample_native_to_crop 2
resample_subfields_native_crop 2
resample_subfields_to_native 2
resample_template_dseg_tissue_for_reg 2
run_inference 2
smooth_surface 4
template_shape_inject 4
template_shape_reg 2
template_xfm_itk2ras 1
unfoldreg_greedy 2
update_native_mesh_structure 4
update_unfold_mesh_structure 8
warp_midthickness_to_inout 8
warp_native_mesh_to_unfold 8
warp_t1_to_corobl_crop 2
warp_unfold_native_to_unfoldreg 2
total 342

Select jobs to execute...
Execute 3 jobs...

[Mon May 12 14:22:32 2025]
localrule cp_template_to_unfold:
input: /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii
output: work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii
jobid: 95
reason: Missing output files: work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii
wildcards: subject=1425, hemi=L, density=0p5mm, label=hipp, surfname=midthickness
resources: tmpdir=/var/folders/1f/_y8ytw7j3tv2pjrzptqrrbx00000gn/T

[Mon May 12 14:22:32 2025]
localrule create_unfold_ref:
output: work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
jobid: 79
reason: Missing output files: work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
wildcards: subject=1425, label=hipp
resources: tmpdir=/var/folders/1f/_y8ytw7j3tv2pjrzptqrrbx00000gn/T

[Mon May 12 14:22:32 2025]
localrule n4_t1:
input: work/sub-1425/anat/sub-1425_T1w.nii.gz
output: sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
jobid: 19
reason: Missing output files: sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
wildcards: subject=1425
threads: 8
resources: tmpdir=/var/folders/1f/_y8ytw7j3tv2pjrzptqrrbx00000gn/T

/bin/bash: wb_command: command not found
/bin/bash: c3d: command not found
/bin/bash: N4BiasFieldCorrection: command not found
RuleException:
CalledProcessError in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/gifti.smk", line 56:
Command 'set -euo pipefail; cp /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii && wb_command -set-structure work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii HIPPOCAMPUS_LEFT -surface-type FLAT -surface-secondary-type MIDTHICKNESS' returned non-zero exit status 127.
[Mon May 12 14:22:32 2025]
Error in rule cp_template_to_unfold:
message: None
jobid: 95
input: /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii
output: work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii
shell:
cp /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii && wb_command -set-structure work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii HIPPOCAMPUS_LEFT -surface-type FLAT -surface-secondary-type MIDTHICKNESS
(command exited with non-zero exit code)
RuleException:
CalledProcessError in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/warps.smk", line 238:
Command 'set -euo pipefail; c3d -create 256x128x16 0.15625x0.15625x0.15625mm -origin 0x200x0mm -orient RPI -o work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz' returned non-zero exit status 127.
[Mon May 12 14:22:32 2025]
Error in rule create_unfold_ref:
message: None
jobid: 79
output: work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
shell:
c3d -create 256x128x16 0.15625x0.15625x0.15625mm -origin 0x200x0mm -orient RPI -o work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
(command exited with non-zero exit code)
RuleException:
CalledProcessError in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/preproc_t1.smk", line 60:
Command 'set -euo pipefail; ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8 N4BiasFieldCorrection -d 3 -i work/sub-1425/anat/sub-1425_T1w.nii.gz -o sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz' returned non-zero exit status 127.
[Mon May 12 14:22:32 2025]
Error in rule n4_t1:
message: None
jobid: 19
input: work/sub-1425/anat/sub-1425_T1w.nii.gz
output: sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
shell:
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8 N4BiasFieldCorrection -d 3 -i work/sub-1425/anat/sub-1425_T1w.nii.gz -o sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
(command exited with non-zero exit code)
Removing output files of failed job cp_template_to_unfold since they might be corrupted:
work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii
Shutting down, this might take some time.
Exiting because a job execution failed. Look below for error messages
[Mon May 12 14:22:32 2025]
Error in rule cp_template_to_unfold:
message: None
jobid: 95
input: /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii
output: work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii
shell:
cp /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-0p5mm_midthickness.surf.gii work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii && wb_command -set-structure work/sub-1425/surf/sub-1425_hemi-L_space-unfold_den-0p5mm_label-hipp_midthickness.surf.gii HIPPOCAMPUS_LEFT -surface-type FLAT -surface-secondary-type MIDTHICKNESS
(command exited with non-zero exit code)
[Mon May 12 14:22:32 2025]
Error in rule create_unfold_ref:
message: None
jobid: 79
output: work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
shell:
c3d -create 256x128x16 0.15625x0.15625x0.15625mm -origin 0x200x0mm -orient RPI -o work/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz
(command exited with non-zero exit code)
[Mon May 12 14:22:32 2025]
Error in rule n4_t1:
message: None
jobid: 19
input: work/sub-1425/anat/sub-1425_T1w.nii.gz
output: sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
shell:
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8 N4BiasFieldCorrection -d 3 -i work/sub-1425/anat/sub-1425_T1w.nii.gz -o sub-1425/anat/sub-1425_desc-preproc_T1w.nii.gz
(command exited with non-zero exit code)
Complete log(s): /Users/ian/Desktop/hippunfold/ds002168_hippunfold/.snakemake/log/2025-05-12T142231.839878.snakemake.log
WorkflowError:
At least one job did not complete successfully.`

[jordandekraker]

these should all download automatically, but previously you would need to append --use-conda. On Fri we merged a PR that removes the need for that flag, so you may need to pull the latest changes (or else append that flag)

[Ian-Goodall-Halliwell]

I just cleared the environment, cleared the conda cache with conda clean -a, then reinstalled as per the instructions.

When running without the --use-conda flag, I get the same error as before. When running with the flag, I get the following error:

(hippunfold-env) ian@Ians-MacBook-Air hippunfold % hippunfold ds002168 ds002168_hippunfold participant --modality T1w --cores all --use-conda

Assuming unrestricted shared filesystem usage.
host: Ians-MacBook-Air.local
Building DAG of jobs...
CyclicGraphException in rule native_metric_to_unfold_nii in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/native_surf.smk", line 1068:
Cyclic dependency on rule native_metric_to_unfold_nii.

CyclicGraphException in rule native_metric_to_unfold_nii in file "/opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/native_surf.smk", line 1068:
Cyclic dependency on rule native_metric_to_unfold_nii.

Your conda installation is not configured to use strict channel priorities. This is however important for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Creating conda environment /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/../envs/nnunet.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /opt/anaconda3/envs/hippunfold-env/lib/python3.12/site-packages/hippunfold/workflow/rules/../envs/nnunet.yaml:
Command:
conda env create --quiet --no-default-packages --file "/Users/ian/Desktop/hippunfold/ds002168_hippunfold/.snakemake/conda/678890ed6ab9b84f9bf8022ff2679112_.yaml" --prefix "/Users/ian/Desktop/hippunfold/ds002168_hippunfold/.snakemake/conda/678890ed6ab9b84f9bf8022ff2679112_"
Output:
/opt/anaconda3/lib/python3.12/argparse.py:2006: FutureWarning: remote_definition is deprecated and will be removed in 25.9. Use conda env create --file=URL instead.
action(self, namespace, argument_values, option_string)
Channels:

• khanlab
• conda-forge
• defaults
  Platform: osx-arm64
  Collecting package metadata (repodata.json): ...working... done
  Solving environment: ...working... failed
  Channels:
• khanlab
• conda-forge
• defaults
  Platform: osx-arm64
  Collecting package metadata (repodata.json): ...working... done
  Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides medpy needed by nnunet-inference-on-cpu-and-gpu-1.6.6-py_0

Could not solve for environment specs
The following package could not be installed
└─ nnunet-inference-on-cpu-and-gpu 1.6.6** is not installable because it requires
└─ medpy, which does not exist (perhaps a missing channel).

[jordandekraker]

@Dhananjhay would you be able to look into this?

[jordandekraker]

I think this is a related issue: Mylla emailed me with this error using the latest singularity container:

App version could not be identified. This usually occurs because the app was not installed with pip. It will be recorded in output as 'unknown'.
Using profiles /src/hippunfold/profiles/workflow/docker-conda and workflow specific profile /src/hippunfold/workflow/profiles/default for setting default command line arguments.
Error: profile given but no config.yaml found. Profile has to be given as either absolute path, relative path or name of a directory available in either /etc/xdg/snakemake or /data/hu_marsiglia/.config/snakemake.

[Dhananjhay]

I think this is a related issue: Mylla emailed me with this error using the latest singularity container:

App version could not be identified. This usually occurs because the app was not installed with pip. It will be recorded in output as 'unknown'.
Using profiles /src/hippunfold/profiles/workflow/docker-conda and workflow specific profile /src/hippunfold/workflow/profiles/default for setting default command line arguments.
Error: profile given but no config.yaml found. Profile has to be given as either absolute path, relative path or name of a directory available in either /etc/xdg/snakemake or /data/hu_marsiglia/.config/snakemake.

Hey Jordan,

This error was caused by an incorrect path pointing to the docker-conda profile in the Dockerfile. I've opened a new PR (#468) to fix the issue.

Thanks, @Ian-Goodall-Halliwell, for bringing this to our attention!

It looks like you're running HippUnfold on a Mac with an M-series chip (arm64 architecture). Unfortunately, many of the packages HippUnfold depends on are not available for arm64, but they are available for the Intel-based architecture (osx-64). You can work around this by using Rosetta 2 emulation:

CONDA_SUBDIR=osx-64 hippunfold ds002168 ds002168_hippunfold participant --modality T1w --cores all --use-conda

However, there's a key limitation: connectome-workbench is currently only available for Linux. As a result, running HippUnfold on macOS is likely to fail unless we make connectome-workbench available for osx-64. I'll start working on that—thanks again!

[Dhananjhay]

Also, there's no need to use the --use-conda flag with the latest hippunfold conda package. Make sure you either uninstall the current hippunfold package or clear the cache before re-installing it again!

[Dhananjhay]

Reopening this since hippunfold conda for OSX is still WIP.