chore: Begin streamlining Docker #84
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@bilgelm Were you able to test this? |
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@effigies it is currently running on the 4D example data that Martin had provided for the sprint, at I'm getting an error when trying to run on a 3D PET image, though, coming from L390 of interfaces.resampling: |
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Getting the same error with the 4D PET image as well, it just takes some time to get there: nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node petref_pet.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 401, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/petprep/interfaces/resampling.py", line 79, in _run_interface
resampled = resample_image(
^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/petprep/interfaces/resampling.py", line 390, in resample_image
mapped_coordinates = ref2vox.map(coordinates)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nitransforms/manip.py", line 155, in map
x = xfm.map(x, inverse=inverse)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nitransforms/linear.py", line 282, in map
return affine.dot(coords).T[..., :-1]
^^^^^^^^^^^^^^^^^^
ValueError: shapes (4,4) and (4619377,3) not aligned: 4 (dim 1) != 4619377 (dim 0)
250819-21:09:27,711 nipype.workflow CRITICAL:
PETPrep failed: Traceback (most recent call last):
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node petref_pet.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 401, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/petprep/interfaces/resampling.py", line 79, in _run_interface
resampled = resample_image(
^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/petprep/interfaces/resampling.py", line 390, in resample_image
mapped_coordinates = ref2vox.map(coordinates)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nitransforms/manip.py", line 155, in map
x = xfm.map(x, inverse=inverse)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/petprep/lib/python3.12/site-packages/nitransforms/linear.py", line 282, in map
return affine.dot(coords).T[..., :-1]
^^^^^^^^^^^^^^^^^^
ValueError: shapes (4,4) and (4619377,3) not aligned: 4 (dim 1) != 4619377 (dim 0)Here's the command I ran: # DATA_DIR is the data Martin provided for the sprint
# DATA_DIR_COPY is just a copy of that so that petprep can write to derivatives/
docker run -ti --rm \
-v $DATA_DIR:/data:ro \
-v $DATA_DIR_COPY/derivatives/freesurfer:/data_fs \
-v $OUTPUT_DIR:/out \
-v $FSLICENSE_DIR:/fslicense \
ghcr.io/nipreps/petprep:maint-streamline /data /out participant \
--skip_bids_validation \
--fs-license-file /fslicense/license.txt \
--fs-no-resume \
--fs-subjects-dir /data_fs \
--pvc-tool petpvc \
--pvc-method GTM \
--pvc-psf 5 \
--ref-mask-name cerebellum \
--ref-mask-index 7 8 46 47 \
-w /out/work --stop-on-first-crash --write-graph |
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I haven't yet started stripping down FreeSurfer, but this includes a few baseline changes that I'd like to ensure don't break things before I do.