Converting main surface: 100% done.
Converting main surface: 100% done.
Converting original surface: 100% done.
Converting pial surface: 100% done.
nquads=4915204, nvertices=592
ERROR: MRISread: file '/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/surf/rh.jacobian_white' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory
Converting main surface: 100% done.
Converting main surface: 100% done.
Converting original surface: 100% done.
Converting pial surface: 100% done.
nquads=4915204, nvertices=592
ERROR: MRISread: file '/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/surf/rh.jacobian_white' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory
reconall_results_path = os.path.join("/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/NIPYPE/diffusion_pipeline/segmentation_stage,"reconall","result_reconall.pklz")
reconall_results = pickle.load(gzip.open(reconall_results_path))
reconall_results_path = os.path.join("/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/NIPYPE/diffusion_pipeline/segmentation_stage","reconall","result_reconall.pklz")
>>> reconall_results_path = os.path.join("/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/NIPYPE/diffusion_pipeline/segmentation_stage","reconall","result_reconall.pklz")
>>>
>>> reconall_results = pickle.load(gzip.open(reconall_results_path))
>>> fs = FreeSurferSource(subjects_dir=reconall_results.outputs.subjects_dir, subject_id=reconall_results.outputs.subject_id)
>>> res = fs.run()
>>> res.outputs.brainmask
u'/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/mri/brainmask.mgz'
>>>
>>> res.outputs.white[1]
u'/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/surf/lh.white'
>>>
>>> res.outputs.T1
u'/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/mri/T1.mgz'
>>>
>>> res.outputs.white[2]
u'/home/gschwind/Documents/CMapper/exampledataset/project01_dsi/connectome_0001/tp1/FREESURFER/surf/rh.jacobian_white'
>>>
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