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docker run -it --rm \
-v /my_input_directory:/bids_dir \
-v /my_output_directory:/output_dir \
-v /Applications/freesurfer/license.txt:/opt/freesurfer/license.txt \
sebastientourbier/multiscalebrainparcellator \
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--thalamic_nuclei \
--hippocampal_subfields \
--brainstem_structures
Is there an error in the command or do you think the outdated version is the problem?
I was also wanting to ask when a new version of the CMP will be available, as I read in the last post that there may be a bug in the current version and I wanted to wait with the installation till the new version is available.
Thanks so much,
David
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docker run -it --rm \ -v /my_input_directory:/bids_dir \
-v /my_output_directory:/output_dir \
-v /Applications/freesurfer/license.txt:/bids_dir/code/license.txt \ sebastientourbier/multiscalebrainparcellator:v1.1.0 \
/bids_dir /output_dir participant --participant_label 01 \ --isotropic_resolution 1.0 \ --thalamic_nuclei \ --hippocampal_subfields \
--brainstem_structures \
----skip_bids_validator
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docker run -it --rm -v /working_directory/ds001:/bids_dir -v /working_directory/ds001/derivatives:/output_dir -v /working_directory/license.txt:/bids_dir/code/license.txt sebastientourbier/multiscalebrainparcellator:v1.1.1 /bids_dir /output_dir participant --participant_label 01 --isotropic_resolution 1.0 --thalamic_nuclei --hippocampal_subfields --brainstem_structures --skip_bids_validator
200506-14:23:21,579 nipype.interface INFO:
> Compute and save jacobian
200506-14:23:21,581 nipype.interface INFO:
... Command: CreateJacobianDeterminantImage 3 "/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcThal/T1_Ind2temp1Warp.nii.gz" "/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcThal/T1_class-thalamus_probtissue_jacobian.nii.gz"
200506-14:23:21,843 nipype.interface INFO:
terminate called after throwing an instance of 'itk::ImageFileReaderException'
what(): /opt/conda/envs/py27msbparc/include/ITK-4.13/itkImageFileReader.hxx:143:
Could not create IO object for reading file /output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcThal/T1_Ind2temp1Warp.nii.gz
The file doesn't exist.
Filename = /output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcThal/T1_Ind2temp1Warp.nii.gz
Aborted
.....
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/cmtklib/parcellation.py", line 1383, in _run_interface
Ij = ni.load(jacobian_file).get_data() # numpy.ndarray
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nibabel/loadsave.py", line 42, in load
raise FileNotFoundError("No such file or no access: '%s'" % filename)
nibabel.py3k.FileNotFoundError: No such file or no access: '/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcThal/T1_class-thalamus_probtissue_jacobian.nii.gz'