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ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0. #1434

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Merged
merged 61 commits into from
Apr 17, 2016
Merged

ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0. #1434

merged 61 commits into from
Apr 17, 2016

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ellisdg
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@ellisdg ellisdg commented Apr 15, 2016

Updates the workflow to check for the FreeSurfer version and change the workflow configuration so that the FS 5.3.0 recon-all equivalent workflow will be run.

David Ellis and others added 30 commits April 13, 2016 15:57
FIX: Fixes a few flags in for FreeSurfer 5.3
2ce38f4
ENH: Print FS version.
7a43049
FIX: Fixes elif syntax error.
ee7ab69
FIX: Adds stop and shrink to autorecon1.
dc8fec3
FIX: Removes entorhinal BA maps for 5.3.
c79f559
FIX: Adds entorhinal to autorecon3
bfa3c29
FIX: Removes thresh.perirhinal from 5.3
291bafd
FIX: Allows for changing of RB atlas
4bd4962
FIX: Fixes input to config for rb_date
c8ddf6d
FIX: config function.
e81d637
FIX: Switches around the intensity normalization for 5.3
97e1021
FIX: fixes connections ar1
c1f8aed
FIX: corrects the output for copy_transform
4d16008
FIX: adds item to outpus for autorecon1
3d60d7d
@ellisdg
FIX: Connects 'nu' of autorecon1 to autorecon2.
06d5fbc
@ellisdg
FIX: Takes out new inputs to CALabel.
759f52e
@ellisdg
FIX: Removes in_aseg from ribbon masking.
a6850ce
@ellisdg
ENH: Allows for implicit aseg input in ribbon masking.
cd7dc15
@ellisdg
FIX: Fixes typo.
c0cf40f
FIX: Fixes source subject for BAMaps thresh.
37fd56c
FIX: Temporary fix for apas2aseg. Will still need to fix what is goin…
1b95329 
…g wrong with aseg.mgz.
FIX: Changes reference of labels to source_fields.
2daa8c1
Fix: turns the mandatory flag off for aseg.
25b7e96
FIX: Fixes failure to copy rh.white
ac60065
FIX: Adds filled input to Aparc2Aseg.
d6560f1
FIX: Allows for aseg to be copied in segstats for 5.3.
9057ffa
FIX: Changes presurf_seg to not being mandatory.
1ec5bf0
FIX: Updates WM_Parcellation_Stats to take aseg as input.
0b6eb84
FIX: Fixes typo when connecting workflows.
987427a
FIX: Fixes error causing sphere.reg to be passed as a label.
2c1c045
David Ellis added 24 commits April 13, 2016 15:58
FIX: Changes .rsplit to os.path.splittext.
6c63ded
FIX: Removes the unnecessary inputs to MakeSurfaces for 53.
848442b
FIX: Allows the interface wrapper to know it is making a pial surface…
1857064 
… for 5.3.0.
FIX: Adds import statement to output aseg function.
ede459f
FIX: Fixes import statement.
a2672c8
FIX: Adds shutil to import for out_aseg function.
775f1f9
FIX: Imports os for out_aseg function.
44f1e29
FIX: fixes bugs in recoding table workflow.
022352c
FIX: Changes nipype.pipeline.Node to pe.Node
f3acecc
FIX: Changes nipype.Node to pe.Node.
7050d57
FIX: Changes nipype.Function to Function.
ccb4b16
FIX: Replaces nipype.IdentityInterface with niu.IdentityInterface.
6c9886f
ENH: Removes the relabels hypointensities for 5.3.
01b84a9
FIX: Switches the presurf labelmap name back to aseg.presurf.mgz.
89e208c
FIX: make check-before-commit
aaf3b05
FIX: switches incorrect if statement.
959c57e
FIX: Fixes aseg input for Aparc2Aseg.
56fbd21
FIX: Adds aseg input for a2009s Aparc2Aseg.
3cd2fd0
FIX: Adds stop and shrink values to autorecon2.py to ensure that the
5644aa2 
6.0beta still works.
FIX: Adds distance to autorecon2.py.
095e359
FIX: Corrected fsvernum if statements to fix 6.0beta workflow.
3f1926c
FIX: Removes duplicate connection.
f88204e
FIX: Changes list position of entorhinal.
58cfc19
DOC: Updates CHANGES
816f787
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Coverage Status

Coverage decreased (-0.003%) to 72.54% when pulling 816f787 on BRAINSia:FreeSurfer53 into 6b0fbaa on nipy:master.

@coveralls
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Coverage Status

Coverage decreased (-0.003%) to 72.54% when pulling 816f787 on BRAINSia:FreeSurfer53 into 6b0fbaa on nipy:master.

@satra
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satra commented Apr 16, 2016

@dgellis90 - because of merging the other PR this one is out of sync with master. could you please merge with master, resolve conflicts and push?

@ellisdg
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ellisdg commented Apr 16, 2016

@satra they are now merged and conflicts resolved.

@satra satra merged commit f6ae4e4 into nipy:master Apr 17, 2016
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@ellisdg @coveralls @satra