Nifti intent codes added to fsl.data.constants. Nifti1 instances have an

'intent' attribute.

fsl/data/constants.py

@@ -79,3 +79,61 @@ NIFTI_XFORM_TALAIRACH    = 3
 
 NIFTI_XFORM_MNI_152      = 4
 """MNI 152 normalized coordinates."""
+
+
+# NIFTI file intent codes
+NIFTI_INTENT_NONE          = 0
+NIFTI_INTENT_CORREL        = 2
+NIFTI_INTENT_TTEST         = 3
+NIFTI_INTENT_FTEST         = 4
+NIFTI_INTENT_ZSCORE        = 5
+NIFTI_INTENT_CHISQ         = 6
+NIFTI_INTENT_BETA          = 7
+NIFTI_INTENT_BINOM         = 8
+NIFTI_INTENT_GAMMA         = 9
+NIFTI_INTENT_POISSON       = 10
+NIFTI_INTENT_NORMAL        = 11
+NIFTI_INTENT_FTEST_NONC    = 12
+NIFTI_INTENT_CHISQ_NONC    = 13
+NIFTI_INTENT_LOGISTIC      = 14
+NIFTI_INTENT_LAPLACE       = 15
+NIFTI_INTENT_UNIFORM       = 16
+NIFTI_INTENT_TTEST_NONC    = 17
+NIFTI_INTENT_WEIBULL       = 18
+NIFTI_INTENT_CHI           = 19
+NIFTI_INTENT_INVGAUSS      = 20
+NIFTI_INTENT_EXTVAL        = 21
+NIFTI_INTENT_PVAL          = 22
+NIFTI_INTENT_LOGPVAL       = 23
+NIFTI_INTENT_LOG10PVAL     = 24
+NIFTI_FIRST_STATCODE       = 2
+NIFTI_LAST_STATCODE        = 24
+NIFTI_INTENT_ESTIMATE      = 1001
+NIFTI_INTENT_LABEL         = 1002
+NIFTI_INTENT_NEURONAME     = 1003
+NIFTI_INTENT_GENMATRIX     = 1004
+NIFTI_INTENT_SYMMATRIX     = 1005
+NIFTI_INTENT_DISPVECT      = 1006
+NIFTI_INTENT_VECTOR        = 1007
+NIFTI_INTENT_POINTSET      = 1008
+NIFTI_INTENT_TRIANGLE      = 1009
+NIFTI_INTENT_QUATERNION    = 1010
+NIFTI_INTENT_DIMLESS       = 1011
+NIFTI_INTENT_TIME_SERIES   = 2001
+NIFTI_INTENT_NODE_INDEX    = 2002
+NIFTI_INTENT_RGB_VECTOR    = 2003
+NIFTI_INTENT_RGBA_VECTOR   = 2004
+NIFTI_INTENT_SHAPE         = 2005
+
+# FSL-specific intent codes
+
+# FNIRT
+FSL_FNIRT_DISPLACEMENT_FIELD            = 2006
+FSL_CUBIC_SPLINE_COEFFICIENTS           = 2007
+FSL_DCT_COEFFICIENTS                    = 2008
+FSL_QUADRATIC_SPLINE_COEFFICIENTS       = 2009
+
+# TOPUP
+FSL_TOPUP_CUBIC_SPLINE_COEFFICIENTS     = 2016
+FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS = 2017
+FSL_TOPUP_FIELD                         = 2018

fsl/data/image.py

@@ -73,6 +73,7 @@ class Nifti1(object):
     ``worldToVoxMat`` A 4*4 array specifying the affine transformation
                       for transforming real world coordinates into voxel
                       coordinates.
+    ``intent``        The NIFTI intent code specified in the header.
     ================= ====================================================
 
     
@@ -100,6 +101,8 @@ class Nifti1(object):
 
         self.header        = header
         self.shape         = shape
+        self.intent        = header.get('intent_code',
+                                        constants.NIFTI_INTENT_NONE)
         self.__origShape   = origShape
         self.pixdim        = pixdim
         self.voxToWorldMat = voxToWorldMat
@@ -115,11 +118,12 @@ class Nifti1(object):
         # We have to treat FSL/FNIRT images
         # specially, as FNIRT clobbers the
         # sform section of the NIFTI header
-        # to store other data. The hard coded
-        # numbers here are the intent codes
-        # output by FNIRT.
+        # to store other data. 
         intent = header.get('intent_code', -1)
-        if intent in (2006, 2007, 2008, 2009):
+        if intent in (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
+                      constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
+                      constants.FSL_DCT_COEFFICIENTS,
+                      constants.FSL_QUADRATIC_SPLINE_COEFFICIENTS):
             log.debug('FNIRT output image detected - using qform matrix')
             voxToWorldMat = np.array(header.get_qform())