If you don't mind one more question for now...
Unless you think I should keep using Cortical Fold Graph 3.0, I would like Morphologist to default to 3.1 so the BSc students have it automatically.
It is no problem to go into CorticalFoldsGraphGeneral.py and change the selection bit like this:
Code: Select all
eNode1 = ParallelExecutionNode( 'CorticalFoldsGraph_3_1', selected=1 )
eNode1.addChild( 'LeftCorticalFoldsGraph_3_1',
ProcessExecutionNode( 'CorticalFoldsGraph', optional = 1 ) )
eNode1.addChild( 'RightCorticalFoldsGraph_3_1',
ProcessExecutionNode( 'CorticalFoldsGraph', optional = 1 ) )
eNode.addChild( 'CorticalFoldsGraph_3_1', eNode1 )
eNode.addChild( 'CorticalFoldsGraph_3_0',
ProcessExecutionNode( 'AnaComputeCorticalFoldArg',
selected=0 ) )
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/home/ericbarnhill/sf_brainvisa-database/RLHanders/r_8_sub2_lhm/t1mri/default_acquisition/default_analysis/nobias_r_8_sub2_lhm.nii.gz
Code: Select all
/home/ericbarnhill/sf_brainvisa-database/RLHanders/r_8_sub2_lhm/t1mri/default_acquisition/default_analysis/folds/3.0/Lr_8_sub2_lhm.arg
So there must be something I need to change, besides the initial selection bit, to make sure the target files also become 3.1 default. I am wondering if I need to change something in this stretch of code, but I am not sure what:
Code: Select all
# links for 3.1 version
eNode.addLink( 'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.mri_corrected',
'mri_corrected' )
eNode.addLink( \
'mri_corrected',
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.mri_corrected' )
eNode.addLink( 'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.split_mask',
'split_mask' )
eNode.addLink( 'split_mask',
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.split_mask' )
eNode.addLink( \
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.commissure_coordinates',
'commissure_coordinates' )
eNode.addLink( \
'commissure_coordinates',
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.commissure_coordinates' )
eNode.addLink( \
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.Talairach_transform',
'Talairach_transform' )
eNode.addLink( \
'Talairach_transform',
'CorticalFoldsGraph_3_1.LeftCorticalFoldsGraph_3_1.Talairach_transform' )
eNode.addLink( \
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.mri_corrected',
'mri_corrected' )
eNode.addLink( \
'mri_corrected',
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.mri_corrected' )
eNode.addLink( 'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.split_mask',
'split_mask' )
eNode.addLink( 'split_mask',
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.split_mask' )
eNode.addLink( \
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.commissure_coordinates',
'commissure_coordinates' )
eNode.addLink( \
'commissure_coordinates',
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.commissure_coordinates' )
eNode.addLink( \
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.Talairach_transform',
'Talairach_transform' )
eNode.addLink( \
'Talairach_transform',
'CorticalFoldsGraph_3_1.RightCorticalFoldsGraph_3_1.Talairach_transform' )
eNode.addLink( 'CorticalFoldsGraph_3_0.mri_corrected', 'mri_corrected' )
eNode.addLink( 'mri_corrected', 'CorticalFoldsGraph_3_0.mri_corrected' )
eNode.addLink( 'CorticalFoldsGraph_3_0.brain_voronoi', 'split_mask' )
eNode.addLink( 'split_mask', 'CorticalFoldsGraph_3_0.brain_voronoi' )
eNode.addLink( 'CorticalFoldsGraph_3_0.Lgraph', 'left_graph' )
eNode.addLink( 'left_graph', 'CorticalFoldsGraph_3_0.Lgraph' )
eNode.addLink( 'CorticalFoldsGraph_3_0.Rgraph', 'right_graph' )
eNode.addLink( 'right_graph', 'CorticalFoldsGraph_3_0.Rgraph' )
eNode.addLink( 'CorticalFoldsGraph_3_0.Commissure_coordinates',
'commissure_coordinates' )
eNode.addLink( 'commissure_coordinates',
'CorticalFoldsGraph_3_0.Commissure_coordinates' )
If it is bad for me to have posted all this code please erase it.
Also please let me know if I should be using 3.0 for now instead.
Merci encore,
Eric