[ENH] Add 3dTnorm interface

Author: Shotgunosine

nipype/interfaces/afni/__init__.py

@@ -16,6 +16,7 @@
                          Maskave, Means, OutlierCount,
                          QualityIndex, ROIStats, Retroicor,
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
+                         TNorm,
                          TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
 from .utils import (ABoverlap, AFNItoNIFTI, Autobox, Axialize, BrickStat, Bucket,

nipype/interfaces/afni/preprocess.py

@@ -2402,6 +2402,67 @@ class TCorrelate(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+class TNormInputSpec(AFNICommandInputSpec):
+    in_file = File(
+        desc='input file to 3dTNorm',
+        argstr='%s',
+        position=-1,
+        mandatory=True,
+        exists=True,
+        copyfile=False)
+    out_file = File(
+        name_template='%s_tnorm',
+        desc='output image file name',
+        argstr='-prefix %s',
+        name_source='in_file')
+    norm2 = traits.Bool(
+        desc='L2 normalize (sum of squares = 1) [DEFAULT]',
+        argstr='-norm2')
+    normR = traits.Bool(
+        desc='normalize so sum of squares = number of time points * e.g., so RMS = 1.',
+        argstr='-normR')
+    norm1 = traits.Bool(
+        desc='L1 normalize (sum of absolute values = 1)',
+        argstr='-norm1')
+    normx = traits.Bool(
+        desc='Scale so max absolute value = 1 (L_infinity norm)',
+        argstr='-normx')
+    polort = traits.Int(
+        desc="""Detrend with polynomials of order p before normalizing
+               [DEFAULT = don't do this]
+             * Use '-polort 0' to remove the mean, for example""",
+        argstr='-polort %s')
+    L1fit = traits.Bool(
+        desc="""Detrend with L1 regression (L2 is the default)
+             * This option is here just for the hell of it""",
+        argstr='-L1fit')
+
+
+class TNorm(AFNICommand):
+    """Shifts voxel time series from input so that seperate slices are aligned
+    to the same temporal origin.
+
+    For complete details, see the `3dTshift Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTshift.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> tnorm = afni.TNorm()
+    >>> tnorm.inputs.in_file = 'functional.nii'
+    >>> tnorm.inputs.norm2 = True
+    >>> tnorm.inputs.out_file = 'rm.errts.unit errts+tlrc'
+    >>> tnorm.cmdline  # doctest: +ALLOW_UNICODE
+    '3dTnorm -norm2 -prefix rm.errts.unit errts+tlrc functional.nii'
+    >>> res = tshift.run()  # doctest: +SKIP
+
+    """
+    _cmd = '3dTnorm'
+    input_spec = TNormInputSpec
+    output_spec = AFNICommandOutputSpec
+
+
 class TShiftInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc='input file to 3dTShift',