I have been trying to get mindboggle to work using the guidelines online (installed python, nipype, docker and mindboggle). When running it, this is what I get:
docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle $IMAGE --id $ID
170922-05:51:34,773 workflow INFO:
Workflow Mindboggle123 settings: [‘check’, ‘execution’, ‘logging’]
170922-05:51:34,814 workflow INFO:
Running serially.
170922-05:51:34,815 workflow INFO:
Executing node recon-all in dir: /home/jovyan/work/mindboggle123_output/working/Mindboggle123/recon-all
170922-05:51:35,31 workflow INFO:
Running: recon-all -all -i S_1OR6QC_T1.nii -subjid Tau -sd /home/jovyan/work/mindboggle123_output/freesurfer_subjects
170922-05:51:35,566 interface INFO:
stdout 2017-09-22T05:51:35.566768:ERROR: cannot find S_1OR6QC_T1.nii
170922-05:51:35,567 interface INFO:
stdout 2017-09-22T05:51:35.566768:Linux 4975161fdabc 4.9.41-moby #1 SMP Wed Sep 6 00:05:16 UTC 2017 x86_64 GNU/Linux
170922-05:51:35,567 interface INFO:
stdout 2017-09-22T05:51:35.566768:
170922-05:51:35,567 interface INFO:
stdout 2017-09-22T05:51:35.566768:recon-all -s exited with ERRORS at Fri Sep 22 05:51:35 UTC 2017
170922-05:51:35,567 interface INFO:
stdout 2017-09-22T05:51:35.566768:
170922-05:51:35,567 interface INFO:
stdout 2017-09-22T05:51:35.566768:For more details, see the log file
170922-05:51:35,568 interface INFO:
stdout 2017-09-22T05:51:35.566768:To report a problem, see http ://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
170922-05:51:35,568 interface INFO:
stdout 2017-09-22T05:51:35.566768:
170922-05:51:36,80 workflow ERROR:
[‘Node recon-all failed to run on host 4975161fdabc.’]
170922-05:51:36,83 workflow INFO:
Saving crash info to /home/jovyan/work/crash-20170922-055136-jovyan-recon-all-ef1f0be4-f490-471b-9753-5dd7b2efc9d2.pklz
170922-05:51:36,83 workflow INFO:
Traceback (most recent call last):
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py”, line 43, in run
node.run(updatehash=updatehash)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 372, in run
self._run_interface()
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 482, in _run_interface
self._result = self._run_command(execute)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 613, in _run_command
result = self._interface.run()
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1081, in run
runtime = self._run_wrapper(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1724, in _run_wrapper
runtime = self._run_interface(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1758, in _run_interface
self.raise_exception(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1682, in raise_exception
**runtime.dictcopy()))
RuntimeError: Command:
recon-all -all -i S_1OR6QC_T1.nii -subjid Tau -sd /home/jovyan/work/mindboggle123_output/freesurfer_subjects
Standard output:
ERROR: cannot find S_1OR6QC_T1.nii
Linux 4975161fdabc 4.9.41-moby #1 SMP Wed Sep 6 00:05:16 UTC 2017 x86_64 GNU/Linux
recon-all -s exited with ERRORS at Fri Sep 22 05:51:35 UTC 2017
For more details, see the log file
To report a problem, see http ://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
Interface ReconAll failed to run.
170922-05:51:36,88 workflow INFO:
Executing node antsCorticalThickness in dir: /home/jovyan/work/mindboggle123_output/working/Mindboggle123/antsCorticalThickness
170922-05:51:36,555 workflow INFO:
Running: antsCorticalThickness.sh -a S_1OR6QC_T1.nii -m /home/jovyan/work/mindboggle123_output/working/Mindboggle123/antsCorticalThickness/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /opt/data/OASIS-30_Atropos_template/T_template0.nii.gz -d 3 -f /opt/data/OASIS-30_Atropos_template/T_template0_BrainCerebellumExtractionMask.nii.gz -s nii.gz -o /home/jovyan/work/mindboggle123_output/ants_subjects/Tau/ants -p nipype_priors/BrainSegmentationPrior%02d.nii.gz -t /opt/data/OASIS-30_Atropos_template/T_template0_BrainCerebellum.nii.gz
170922-05:51:36,610 interface INFO:
stdout 2017-09-22T05:51:36.610535:The specified image “S_1OR6QC_T1.nii” does not exist.
170922-05:51:37,624 workflow ERROR:
[‘Node antsCorticalThickness failed to run on host 4975161fdabc.’]
170922-05:51:37,625 workflow INFO:
Saving crash info to /home/jovyan/work/crash-20170922-055137-jovyan-antsCorticalThickness-f699c60d-a7d8-4251-a295-536be0a88a03.pklz
170922-05:51:37,625 workflow INFO:
Traceback (most recent call last):
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py”, line 43, in run
node.run(updatehash=updatehash)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 372, in run
self._run_interface()
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 482, in _run_interface
self._result = self._run_command(execute)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py”, line 613, in _run_command
result = self._interface.run()
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1081, in run
runtime = self._run_wrapper(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1724, in _run_wrapper
runtime = self._run_interface(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/ants/segmentation.py”, line 551, in _run_interface
runtime = super(CorticalThickness, self)._run_interface(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1758, in _run_interface
self.raise_exception(runtime)
File “/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py”, line 1682, in raise_exception
**runtime.dictcopy()))
RuntimeError: Command:
antsCorticalThickness.sh -a S_1OR6QC_T1.nii -m /home/jovyan/work/mindboggle123_output/working/Mindboggle123/antsCorticalThickness/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /opt/data/OASIS-30_Atropos_template/T_template0.nii.gz -d 3 -f /opt/data/OASIS-30_Atropos_template/T_template0_BrainCerebellumExtractionMask.nii.gz -s nii.gz -o /home/jovyan/work/mindboggle123_output/ants_subjects/Tau/ants -p nipype_priors/BrainSegmentationPrior%02d.nii.gz -t /opt/data/OASIS-30_Atropos_template/T_template0_BrainCerebellum.nii.gz
Standard output:
The specified image “S_1OR6QC_T1.nii” does not exist.
Standard error:
Return code: 1
Interface antsCorticalThickness failed to run.
170922-05:51:37,630 workflow INFO:
***********************************
170922-05:51:37,630 workflow ERROR:
could not run node: Mindboggle123.recon-all
170922-05:51:37,630 workflow INFO:
crashfile: /home/jovyan/work/crash-20170922-055136-jovyan-recon-all-ef1f0be4-f490-471b-9753-5dd7b2efc9d2.pklz
170922-05:51:37,630 workflow ERROR:
could not run node: Mindboggle123.antsCorticalThickness
170922-05:51:37,630 workflow INFO:
crashfile: /home/jovyan/work/crash-20170922-055137-jovyan-antsCorticalThickness-f699c60d-a7d8-4251-a295-536be0a88a03.pklz
170922-05:51:37,630 workflow INFO:
***********************************
Traceback (most recent call last):
File “/opt/conda/bin/mindboggle123”, line 311, in
mbFlow.run(plugin=args.plugin)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/workflows.py”, line 590, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py”, line 61, in run
report_nodes_not_run(notrun)
File “/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/base.py”, line 101, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. ’
RuntimeError: Workflow did not execute cleanly. Check log for details
What am i doing wrong?