rcruces
commented
11 months ago Hello, maybe the issue is because directories that are not correctly being mounted inside the singularity container. Perhaps you can try to use the option -B
-B, --bind strings a user-bind path specification.
spec has the format
src[:dest[:opts]], where src and
dest are outside and inside paths.
If dest is not given, it is set
equal to src. Mount options
('opts') may be specified as 'ro'
(read-only) or 'rw' (read/write,
which is the default). Multiple bind
paths can be given by a comma
separated list.Like here:
micapipe_image=/home/mm2075/rds/hpc-work/Pipelines/micapipe/micalab_micapipe_v0.2.2-2023-08-04-c796d70fe910.simg
singularity run --cleanenv \
-B ${bids_dir}:/bids\
-B ${out_dir}:/out \
-B ${temp_dir}/work_dir/sub-${subj}_ses-${session}:/tmp \
-B /home/mm2075/rds/hpc-work/Pipelines/license.txt:/opt/licence.txt \
${micapipe_image} -bids /bids -out /out -tmpDir /tmp -fs_licence /opt/licence.txt \
-sub ${subj} -ses ${session} \
-proc_structuralYou can also increase the number of threads with -threads for faster computation, the default is 6. Let me know if it works. Also could you download the latest dockerhub container, we had a typo in one module and we replace the image yesterday.
Additionally what is the log of this COMMAND --> 3dresample? which is previous of fslreorient2std. It looks like there is something missing on fslpython. I just ran two test on two different datasets and I could not replicated that python error.
ModuleNotFoundError: No module named 'numpy.testing.decorators'
marcellamontagnese
araikes
Hi, Thanks so much for developing such a useful multimodal pipeline!
I just started using this and I am trying to run the following command from the HPC:
singularity run --cleanenv /home/mm2075/rds/hpc-work/Pipelines/micapipe/micalab_micapipe_v0.2.2-2023-08-04-c796d70fe910.simg \ -bids ${bids_dir} \ -sub ${subj} \ -out ${out_dir} \ -ses ${session} \ -tmpDir ${temp_dir}/work_dir/sub-${subj}_ses-${session} \ -fs_licence /home/mm2075/rds/hpc-work/Pipelines/license.txt \ -proc_structuralHowever the pipeline stops within a few seconds with error:
[ ERROR ]..... sub-33909_ses-20220505_space-nativepro_T1w was not generatedIt seems to not be able to locate files correctly and fails at several steps based on the output below:mm2075 @ login-e-2 Wed Aug 9 16:46:24 BST 2023: COMMAND --> fslreorient2std /rds/user/mm2075/hpc-work/Pipelines/micapipe/work_dir/sub-33909_ses-20220505/21176_micapipe_proc_struc-vol_33909/obl-33909_ses-20220505_T1w.nii.gz /rds/user/mm2075/hpc-work/Pipelines/micapipe/work_dir/sub-33909_ses-20220505/21176_micapipe_proc_struc-vol_33909/reo-33909_ses-20220505_T1w.nii.gzTraceback (most recent call last): File "/opt/fsl-6.0.2/bin/imcp", line 6, in <module> from fsl.scripts.imcp import main File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/fsl/scripts/imcp.py", line 26, in <module> import fsl.utils.imcp as imcp File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/fsl/utils/imcp.py", line 21, in <module> import nibabel as nib File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/nibabel/__init__.py", line 38, in <module> from . import analyze as ana File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/nibabel/analyze.py", line 87, in <module> from .volumeutils import (native_code, swapped_code, make_dt_codes, File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/nibabel/volumeutils.py", line 22, in <module> from .casting import (shared_range, type_info, OK_FLOATS) File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/nibabel/casting.py", line 11, in <module> from .testing import setup_test # noqa File "/opt/fsl-6.0.2/fslpython/envs/fslpython/lib/python3.7/site-packages/nibabel/testing/__init__.py", line 21, in <module> from numpy.testing.decorators import skipif ModuleNotFoundError: No module named 'numpy.testing.decorators'Thanks a lot for the help!