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ENH: Enable recon-all -FLAIR / -FLAIRpial options #2279

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Merged
merged 3 commits into from
Nov 13, 2017
Merged

ENH: Enable recon-all -FLAIR / -FLAIRpial options #2279

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edece6e
ENH: Enable recon-all -FLAIR/-FLAIRpial
effigies Nov 13, 2017
56e9613
make specs
effigies Nov 13, 2017
77f5bd4
FIX: T2/FLAIR inputs not mutually exclusive
effigies Nov 13, 2017
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13 changes: 10 additions & 3 deletions nipype/interfaces/freesurfer/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -628,10 +628,17 @@ class ReconAllInputSpec(CommandLineInputSpec):
argstr="-hemi %s")
T1_files = InputMultiPath(File(exists=True), argstr='-i %s...',
desc='name of T1 file to process')
T2_file = File(exists=True, argstr="-T2 %s", min_ver='5.3.0',
T2_file = File(exists=True, argstr="-T2 %s",
min_ver='5.3.0',
desc='Convert T2 image to orig directory')
use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0',
desc='Use converted T2 to refine the cortical surface')
FLAIR_file = File(exists=True, argstr="-FLAIR %s",
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can we use a single input i.e. T2, perhaps with:

  1. a requires set for use*
  2. a description update saying T2 file can be T2 or FLAIR
    ?

freesurfer doesn't really distinguish between the inputs in the recon-all process, only the use options change some thresholds to fixing surfaces.

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When adding the images, -T2 <file> vs -FLAIR <file> dictates whether it's converted to orig/T2raw.mgz or orig/FLAIRraw.mgz Then -T2pial and -FLAIRpial draw from those files as well as set different options to mris_make_surfaces. (Also note that -T2 and -FLAIR are not mutually exclusive, but -T2pial and -FLAIRpial are.)

Also, recall that someone may use this in multiple stages. The -T2 <file> and -T2pial options may not be passed in the same interface, so dependencies between these options aren't necessarily going to be straightforward.

Given these considerations, do you see a way of simplifying this?

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@effigies - i was going to say we could set the appropriate argument in _format_arg. but since this interface offers the possibility of passing any of the Do* arguments, perhaps this is cleaner at this point. so i'm ok with the way this PR is currently implemented.

min_ver='5.3.0',
desc='Convert FLAIR image to orig directory')
use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0', xor=['use_FLAIR'],
desc='Use T2 image to refine the pial surface')
use_FLAIR = traits.Bool(argstr="-FLAIRpial",
min_ver='5.3.0', xor=['use_T2'],
desc='Use FLAIR image to refine the pial surface')
openmp = traits.Int(argstr="-openmp %d",
desc="Number of processors to use in parallel")
parallel = traits.Bool(argstr="-parallel",
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10 changes: 9 additions & 1 deletion nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
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Expand Up @@ -4,7 +4,10 @@


def test_ReconAll_inputs():
input_map = dict(T1_files=dict(argstr='-i %s...',
input_map = dict(FLAIR_file=dict(argstr='-FLAIR %s',
min_ver='5.3.0',
),
T1_files=dict(argstr='-i %s...',
),
T2_file=dict(argstr='-T2 %s',
min_ver='5.3.0',
Expand Down Expand Up @@ -108,8 +111,13 @@ def test_ReconAll_inputs():
terminal_output=dict(deprecated='1.0.0',
nohash=True,
),
use_FLAIR=dict(argstr='-FLAIRpial',
min_ver='5.3.0',
xor=['use_T2'],
),
use_T2=dict(argstr='-T2pial',
min_ver='5.3.0',
xor=['use_FLAIR'],
),
xopts=dict(argstr='-xopts-%s',
),
Expand Down