From 3591a768f78dc77ae9ef7082561e6560d8f55000 Mon Sep 17 00:00:00 2001
From: Nicolas Toussaint <n.toussaint@ucl.ac.uk>
Date: Mon, 11 Jan 2016 11:39:06 +0000
Subject: [PATCH] niftyfit interface - ASL processing: adding te fit_qt1
 interface to the lot, this interface is used to estimate the m0 map from the
 inversion recovery image

---
 nipype/interfaces/niftyfit/__init__.py |  1 +
 nipype/interfaces/niftyfit/qt1.py      | 73 ++++++++++++++++++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 nipype/interfaces/niftyfit/qt1.py

diff --git a/nipype/interfaces/niftyfit/__init__.py b/nipype/interfaces/niftyfit/__init__.py
index 6e4361a102..d84fd451f6 100644
--- a/nipype/interfaces/niftyfit/__init__.py
+++ b/nipype/interfaces/niftyfit/__init__.py
@@ -8,3 +8,4 @@
 from .base import (Info)
 from .dwi import (FitDwi, DwiTool)
 from .asl import (FitAsl)
+from .qt1 import (FitQt1)
diff --git a/nipype/interfaces/niftyfit/qt1.py b/nipype/interfaces/niftyfit/qt1.py
new file mode 100644
index 0000000000..6505719b03
--- /dev/null
+++ b/nipype/interfaces/niftyfit/qt1.py
@@ -0,0 +1,73 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""The QT1 module of niftyfit, which wraps the Multi-Echo T1 fitting methods in NiftyFit.
+"""
+
+from nipype.interfaces.niftyfit.base import getNiftyFitPath,NIFTYFITCommandInputSpec, NIFTYFITCommand
+from nipype.interfaces.base import (TraitedSpec, File, traits, isdefined)
+
+#-----------------------------------------------------------
+# FitAsl wrapper interface
+#-----------------------------------------------------------
+
+# Input spec
+class FitQt1InputSpec(NIFTYFITCommandInputSpec):
+
+    source_file = File(exists=True, desc='Filename of the 4D Multi-Echo T1 source image (mandatory)',
+                       argstr='-source %s', mandatory=True)
+
+# *** Output options:
+    t1map = File(genfile=True, exists=True, desc='Filename of the estimated output T1 map (in ms).',
+                 argstr='-t1map %s', name_source=['source_file'], name_template='%s_t1map')
+    m0map = File(genfile=True, exists=True, desc='Filename of the estimated input M0 map.',
+                 argstr='-m0map %s', name_source=['source_file'], name_template='%s_m0map')
+    mcmap = File(genfile=True, exists=True, desc='Filename of the estimated output multi-parameter map.',
+                 argstr='-mcmap %s', name_source=['source_file'], name_template='%s_mcmap')
+    error_file = File(genfile=True, exists=True, desc='Filename of the error map (symmetric matrix, [Diag,OffDiag]).',
+                      argstr='-error %s', name_source=['source_file'], name_template='%s_error')
+    syn_file = File(genfile=True, exists=True, desc='Filename of the synthetic ASL data.',
+                    argstr='-syn %s', name_source=['source_file'], name_template='%s_syn')
+    res_file = File(genfile=True, exists=True, desc='Filename of the model fit residuals',
+                    argstr='-res %s', name_source=['source_file'], name_template='%s_res')
+
+# *** Experimental options (Choose those suitable for the model!):
+    mask = File(exists=True, desc='Filename of image mask.',
+                argstr='-mask %s')
+    prior = File(exists=True, desc='Filename of parameter prior.',
+                 argstr='-prior %s')
+    TE = traits.Float(desc='TE Echo Time [0ms!].', argstr='-TE %f')
+    TR = traits.Float(desc='TR Repetition Time [10s!].', argstr='-TR %f')
+
+# IR options:
+
+    SR = traits.Bool(desc='Saturation Recovery fitting [default].', argstr='-SR')
+    IR = traits.Bool(desc='Inversion Recovery fitting [default].', argstr='-SR')
+    T1s = traits.ListFloat(desc='Inversion times for T1 data as a list (in s)', argstr='-T1s %f %f %f')
+    T1Lists = traits.File(exists=True, desc='Filename of list of pre-defined TIs', argstr='-T1List %s')
+
+# SPGR options
+    SPGR = traits.Bool(desc='Spoiled Gradient Echo fitting', argstr='-SPGR')
+
+# Output spec
+class FitQt1OutputSpec(TraitedSpec):
+    t1map = File(exists=True, desc='Filename of the estimated output T1 map (in ms)')
+    m0map = File(exists=True, desc='Filename of the m0 map')
+    mcmap = File(exists=True, desc='Filename of the estimated output multi-parameter map')
+    error_file = File(exists=True, desc='Filename of the error map (symmetric matrix, [Diag,OffDiag])')
+    syn_file = File(exists=True, desc='Filename of the synthetic ASL data')
+    res_file = File(exists=True, desc='Filename of the model fit residuals')
+
+# FitAsl function
+class FitQt1(NIFTYFITCommand):
+    """ Use NiftyFit to perform ASL fitting.
+    
+    Examples
+    --------
+    
+    >>> from nipype.interfaces import niftyfit
+    """
+    _cmd = getNiftyFitPath('fit_qt1')
+    input_spec = FitQt1InputSpec
+    output_spec = FitQt1OutputSpec
+    
+    _suffix = '_fit_qt1'