Closed JohnGriffiths closed 7 years ago
according to this:
there should be a ROIv file.
Thanks Satra.
I think I see the problem now.
Looks like there should only be an ROIv file if 'dilation == True'
I had it set to false (the default), and it was still being expected for some reason.
Re-running now with dilation=True...
I have the same problem as @JohnGriffiths. I have FSL 5.0 and Freesurfer 5-20130513. Everything else is updated to the latest version. I am following the guide at:
http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity_advanced.html
I tried everything on a Linux Mint platform. When this didn't work, I then tried using the NeuroDebian 7.2.0 virtual machine. Same problem.
Crash file:
Node: connectivity.mapping.Parcellate.a0
Working directory: /usr/local/freesurfer/dmri_connectivity_advanced/connectivity/mapping/_subject_id_subj1/Parcellate
Node inputs:
dilation = False
freesurfer_dir = <undefined>
ignore_exception = False
out_roi_file = <undefined>
parcellation_name = scale500
subject_id = subj1
subjects_dir = /usr/local/freesurfer/subjects
Traceback:
Traceback (most recent call last):
File "/usr/lib/pymodules/python2.7/nipype/pipeline/plugins/linear.py", line 37, in run
node.run(updatehash=updatehash)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1282, in run
self._run_interface()
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1380, in _run_interface
self._result = self._run_command(execute)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1504, in _run_command
result = self._interface.run()
File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 895, in run
runtime = self._run_interface(runtime)
File "/usr/lib/pymodules/python2.7/nipype/interfaces/cmtk/parcellation.py", line 586, in _run_interface
crop_and_move_datasets(self.inputs.subject_id, self.inputs.subjects_dir, self.inputs.freesurfer_dir, self.inputs.parcellation_name, self.inputs.out_roi_file)
File "/usr/lib/pymodules/python2.7/nipype/interfaces/cmtk/parcellation.py", line 477, in crop_and_move_datasets
raise Exception('File %s does not exist.' % d[0])
Exception: File ./ROIv_scale500.nii.gz does not exist.
Interface Parcellate failed to run.
@satra If it helps, here is what is happening just before it fails:
reading template info from volume /usr/local/freesurfer/subjects/subj1/mri/orig/001.mgz...
INFO : 2013-11-28 01:38:49,337 : main : reading template info from volume /usr/local/freesurfer/subjects/subj1/mri/orig/001.mgz...
INFO : 2013-11-28 01:38:49,337 : main : reading template info from volume /usr/local/freesurfer/subjects/subj1/mri/orig/001.mgz...
INFO : 2013-11-28 01:38:49,337 : main : reading template info from volume /usr/local/freesurfer/subjects/subj1/mri/orig/001.mgz...
INFO : 2013-11-28 01:38:49,337 : main : reading template info from volume /usr/local/freesurfer/subjects/subj1/mri/orig/001.mgz...
131128-01:38:49,337 main INFO:
Reslicing using nearest
INFO : 2013-11-28 01:38:49,337 : main : Reslicing using nearest
INFO : 2013-11-28 01:38:49,337 : main : Reslicing using nearest
INFO : 2013-11-28 01:38:49,337 : main : Reslicing using nearest
INFO : 2013-11-28 01:38:49,337 : main : Reslicing using nearest
131128-01:38:49,337 main INFO:
writing to ./ROI_HR_th.nii.gz...
INFO : 2013-11-28 01:38:49,337 : main : writing to ./ROI_HR_th.nii.gz...
INFO : 2013-11-28 01:38:49,337 : main : writing to ./ROI_HR_th.nii.gz...
INFO : 2013-11-28 01:38:49,337 : main : writing to ./ROI_HR_th.nii.gz...
INFO : 2013-11-28 01:38:49,337 : main : writing to ./ROI_HR_th.nii.gz...
131128-01:38:49,338 runCmd DEBUG:
Return Value: 0
DEBUG : 2013-11-28 01:38:49,338 : runCmd : Return Value: 0
DEBUG : 2013-11-28 01:38:49,338 : runCmd : Return Value: 0
DEBUG : 2013-11-28 01:38:49,338 : runCmd : Return Value: 0
DEBUG : 2013-11-28 01:38:49,338 : runCmd : Return Value: 0
131128-01:38:49,338 interface INFO:
Processing ./ROIv_scale500.nii.gz:
INFO : 2013-11-28 01:38:49,338 : interface : Processing ./ROIv_scale500.nii.gz:
INFO : 2013-11-28 01:38:49,338 : interface : Processing ./ROIv_scale500.nii.gz:
INFO : 2013-11-28 01:38:49,338 : interface : Processing ./ROIv_scale500.nii.gz:
INFO : 2013-11-28 01:38:49,338 : interface : Processing ./ROIv_scale500.nii.gz:
131128-01:38:49,339 workflow ERROR:
['Node Parcellate.a0 failed to run on host neurodebian.']
ERROR : 2013-11-28 01:38:49,339 : workflow : ['Node Parcellate.a0 failed to run on host neurodebian.']
ERROR : 2013-11-28 01:38:49,339 : workflow : ['Node Parcellate.a0 failed to run on host neurodebian.']
ERROR : 2013-11-28 01:38:49,339 : workflow : ['Node Parcellate.a0 failed to run on host neurodebian.']
ERROR : 2013-11-28 01:38:49,339 : workflow : ['Node Parcellate.a0 failed to run on host neurodebian.']
131128-01:38:49,364 workflow INFO:
Saving crash info to /usr/local/freesurfer/crash-20131128-013849-brain-Parcellate.a0.npz
INFO : 2013-11-28 01:38:49,364 : workflow : Saving crash info to /usr/local/freesurfer/crash-20131128-013849-brain-Parcellate.a0.npz
INFO : 2013-11-28 01:38:49,364 : workflow : Saving crash info to /usr/local/freesurfer/crash-20131128-013849-brain-Parcellate.a0.npz
INFO : 2013-11-28 01:38:49,364 : workflow : Saving crash info to /usr/local/freesurfer/crash-20131128-013849-brain-Parcellate.a0.npz
INFO : 2013-11-28 01:38:49,364 : workflow : Saving crash info to /usr/local/freesurfer/crash-20131128-013849-brain-Parcellate.a0.npz
There is a _ROIscale500.nii.gz file located at:
./dmri_connectivity_advanced/connectivity/mapping/_subject_id_subj1/Parcellate/ROI_scale500.nii.gz
But there is no _ROIvscale500.nii.gz file anywhere.
Any suggestions would be very much appreciated.
@swederik - hey erik, could you take a look at this to see if you can spot sth obvious?
Thank you, I will try it.
Had an error come up in the Parcellate node when using a variant on the mrtrix connectivity workflow.
Exception: File ./ROIv_scale500.nii.gz does not exist. Interface Parcellate failed to run. Inputs: dilation = False freesurfer_dir =
ignore_exception = False
out_roi_file =
parcellation_name = scale500
subject_id = CBU080541
subjects_dir = /work/imaging5/Freesurfer
There is an 'ROI_scale500.nii.gz' file, but not an 'ROIv_scale500.nii.gz'.
What are 'ROIv_files', as opposed to 'ROI_files' ? They only seem to come up in the parcellate node. Can't quite tell if it's a typo or if there's some functional significance that I am missing.
See here
https://github.com/nipy/nipype/blob/9595f272aa4086ea28f7534a8bd05690f60bf6b8/nipype/interfaces/cmtk/parcellation.py#L552
e.g. outputs['roiv_file'] = op.abspath(self._gen_outfilename( 'nii.gz', 'ROIv'))
So
a) is this a bug?
and if so
b) any simple things I can do to work around it without changing the code?
Ta.
John