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Merged
merged 130 commits into from
Apr 6, 2016
Merged

ENH: FreeSurfer Wrappings for Recon-All Workflow #1326

merged 130 commits into from
Apr 6, 2016

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ellisdg
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@ellisdg ellisdg commented Jan 21, 2016

This pull request add the wrappings for the following FreeSurfer commands:

  • mri_nu_correct.mni
  • mri_watershed
  • mri_normalize
  • mri_ca_normalize
  • mri_ca_register
  • mri_ca_label
  • mris_ca_label
  • mri_cc
  • mri_segment
  • mri_edit_wm_with_aseg
  • mri_concatenate_lta
  • mri_label2label
  • mris_label2annot
  • mris_spherical_average
  • mri_add_xform_to_header
  • talairach_afd
  • talairach_avi
  • tal_QC_AZS
  • mri_remove_neck
  • mri_fill
  • mris_inflate
  • mris_sphere
  • mris_fix_topology
  • mris_euler_number
  • mris_remove_intersection
  • mris_make_surfaces
  • mris_curvature
  • mris_curvature_stats
  • mris_jacobian
  • mris_calc
  • mris_volmask
  • mris_anatomical_stats
  • pctsurfcon
  • mri_relabel_hypointensities
  • mri_aparc2aseg
  • apas2aseg
  • mri_robust_template
  • mri_fuse_segmentations
  • mpr2mni305
  • avi2talxfm
  • mri_em_register
  • mris_register
  • mrisp_paint

This pull requests also adds inputs to some of the existing wrappings for FreeSurfer commands. These wrappings and changes were needed to create a a recon-all workflow in nipype that performs the same steps as recon-all. The workflows and usage information can be found here:
https://github.com/BRAINSia/BRAINSTools/tree/FreeSurferBreakout/AutoWorkup/fs_nipype

David Ellis added 30 commits January 19, 2016 09:58
ENH: adds support for FS commands that utilize OpenMP
0ebb5da
DOC: Changes description of --conform flag to be consistent with FS d…
758184b 
…ocumentation
ENH: adds flag to MRIConvert to conform image to dimensions of 256^3
2102a39
ENH: Adds wrapping for command "mri_nu_correct.mni" as MNIBiasCorrection
14f4728 
Author: David Welch
ENH: Adds wrapping for mri_watershed
6fa7aa6 
Author: David Welch
ENH: Adds wrapping for FS command "mri_normalize"
be9b1cd 
Author: David Welch
ENH: Adds wrapping for FS command "mri_ca_normalize"
0d308f1 
Author: David Ellis
ENH: Adds wrapping for FS command "mri_ca_register"
b5b86de 
Author: David Ellis
ENH: Adds wrappings for FS commands "mri_ca_label" and "mris_ca_label"
b0839ce
ENH: Adds wrappings for FS commands "mri_cc" and "mri_segment"
ef611e3
ENH: Adds wrapping for SF command "mri_edit_wm_with_aseg"
556459b
ENH: Adds wrapping for FS command "mri_concatenate_lta"
7acb831
FIX: Imports traits to FS base.py
9294969
FIX: Adds the new FS command wrappers to the init file.
29ad6b3
DOC: updates doc tests for new FS wrapper classes
313ec71
ENH: Extends MRIPreproc so that it can be used in a recon-all workflow
18a9ff6
BUG: fixes the partial_volume_file input for SegStats
699effb
ENH: Adds empty flag to SegStats
23c9ead
ENH: Adds inputs brainmask_file, etiv, etiv_only, vox, supratent, sub…
3fc42ec 
…cort_gm, total_gray, euler,

in_intensity, and intensity_units to SegStatsInputSpec.
ENH: Adds formatting for argstr of 'in_intensity' input for SegStats
9f48e45
ENH: Adds SegStatsReconAll and SegStatsReconAllInputSpec to extend Se…
819c668 
…gStats and SegStatsInputSpec for use in a recon-all workflow.
DOC: Changes inputs for SegStatsReconAll doc tests and removes any sk…
f9b9ca5 
…ipping of its doctesting.
ENH: Adds FS wrapping for 'mri_label2label'
6ef623c
ENH: Adds FS wrapping for 'mris_label2annot'
d8daf56
ENH: Adds FS wrapping for 'mris_spherical_average'
cdd4938
FIX: Adds the new FS wrappings from model.py to the __init__.py file
e2ef637
ENH: Adds inputs 'keep_mask_deletion_edits' and 'transfer' to ApplyMask
9226772
FIX: Fixes the inputs of SmoothTesselation to be consistent with the …
623bf5d 
…documentation for 'mris_smooth'

The only positional arguments according to the documentation should be in_file and out_file.
The position for these inputs should be -2 and -1, respectively.
Other options do not require a fixed position.
Defaults are set automatically by 'mris_smooth' and do not need to be written into the nipype wrappings.
ENH: Adds input 'seed' which enables seed for setting random number g…
3df253d 
…enerator.
ENH: Adds FS wrapping for "mri_add_xform_to_header"
02cb151 
Author: David Welch
@coveralls
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Coverage Status

Changes Unknown when pulling 46a3042 on BRAINSia:FreeSurferBreakout into * on nipy:master*.

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Coverage Status

Changes Unknown when pulling c2bdc66 on BRAINSia:FreeSurferBreakout into * on nipy:master*.

@ellisdg
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ellisdg commented Mar 29, 2016

@satra I added the freesurfer workflows and created an example (smri_fsreconall.py), but the cicleci tests are failing because during workflow setup, I require that the FREESURFER_HOME environmental variable be set. Should I just remove this requirement, or is there a way that I can get around this?

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Coverage Status

Changes Unknown when pulling b54c79f on BRAINSia:FreeSurferBreakout into * on nipy:master*.

@ellisdg
FIX: Changes the implementation for checking the environemntal variab…
8cde742 
…les so that it doesn't produce an error (just a warning) when testing without freesurfer.
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Coverage Status

Changes Unknown when pulling 8cde742 on BRAINSia:FreeSurferBreakout into * on nipy:master*.

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Coverage Status

Changes Unknown when pulling 07060d4 on BRAINSia:FreeSurferBreakout into * on nipy:master*.

@ellisdg
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ellisdg commented Mar 31, 2016

@satra I added name source to simplify a lot of the interfaces. I also added an example workflow that runs recon-all on two subjects from the tutorial data and then gets the average subject. Everything works when running the workflow using FreeSurfer 6.0 and the outputs look identical to the standard recon-all workflow.

@satra
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satra commented Mar 31, 2016

@dgellis90 - can you update the CHANGES file and push. i will merge it.

the freesurfer beta was yanked and they are planning to release 6.0 sometime before ohbm. have you tested this at all with freesurfer 5.3?

@ellisdg
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ellisdg commented Mar 31, 2016

@satra I had been doing all my testing in 6.0 beta thinking it would be released soon. So I'll run some tests over the next few days and see if I can get it running on 5.3 as well.

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satra commented Mar 31, 2016

@dgellis90 - you will also need to merge with current master, you probably have an older version of the CHANGES file.

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Coverage Status

Coverage increased (+0.04%) to 73.019% when pulling 4b850c8 on BRAINSia:FreeSurferBreakout into c46b932 on nipy:master.

@satra satra merged commit ee871ba into nipy:master Apr 6, 2016
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satra commented Apr 6, 2016

@dgellis90 - let us know how tests with 5.3 go

@hjmjohnson
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@satra David and I discussed this today, and we hope that it will be completed yet this week.

@hjmjohnson hjmjohnson deleted the FreeSurferBreakout branch April 6, 2016 02:46
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5 participants
@ellisdg @satra @chrisgorgo @hjmjohnson @coveralls