Fix DTI protocol (#228) (#229)

* Update reslicing to use new `mrgrid` command

This also works with older `mrreslice`

* Fix bad indent in tensorReorder()

* Update documentation

Author: TheJaeger

CHANGELOG.rst

@@ -4,6 +4,26 @@ Changelog
 All notable changes to this project will be documented in this file or
 page
 
+`v1.0_RC4`_
+-----------
+
+Sep 22, 2020
+
+**Added**:
+
+* Reslicing compatibility udpated for new MRTrix3 version
+  where ``mrrelice`` has been changed to ``mrgrid``.
+  PyDesigner will work with either versions.
+
+**Changed**:
+
+* Fixed a bad indent in tensor reordering function
+  that produced an error in DTI protocols.
+
+**Removed**:
+
+* None
+
 `v1.0_RC3`_
 -----------
 
@@ -198,6 +218,7 @@ Initial port of MATLAB code to Python. 200,000,000,000 BCE
 
 .. Links
 
+.. _v1.0_RC4: https://github.com/m-ama/PyDesigner/releases/tag/v1.0_RC4
 .. _v1.0_RC3: https://github.com/m-ama/PyDesigner/releases/tag/v1.0_RC3
 .. _v1.0_RC2: https://github.com/m-ama/PyDesigner/releases/tag/v1.0_RC2
 .. _v1.0_RC1: https://github.com/m-ama/PyDesigner/releases/tag/v1.0-RC1

designer/fitting/dwipy.py

@@ -2576,7 +2576,7 @@ def tensorReorder(self, dwiType):
             dt[20, :] = self.dt[14, :]      # K14
             DT = vectorize(dt[0:6, :], self.mask)
             KT = vectorize(dt[6:21, :], self.mask)
-            return DT, KT
+        return DT, KT
 
     def irllsviolmask(self, reject):
         """

designer/info.py

@@ -10,7 +10,7 @@
     )
 )
 __packagename__ = 'PyDesigner'
-__version__='v1.0-RC3'
+__version__='v1.0-RC4'
 __author__ = 'PyDesigner developers'
 __copyright__ = 'Copyright 2020, PyDesigner developers, MUSC Advanced Image Analysis (MAMA)'
 __credits__ = [

designer/preprocessing/mrpreproc.py

@@ -953,16 +953,33 @@ def reslice(input, output, size, interp='linear',
             'reslicing'.format(specified_size, current_size))
         copyfile(input, output)
         return
-    arg = ['mrresize']
+    arg = []
+    if which('mrresize') is None:
+        arg.extend(
+            [
+                'mrgrid',
+                input,
+                'regrid',
+                dim_str, size,
+                '-interp', interp,
+                output
+            ]
+        )
+    else:
+        arg.extend(
+            [
+                'mrresize',
+                dim_str, size,
+                '-interp', interp,
+                input, output
+            ]
+        )
     if force:
         arg.append('-force')
     if not verbose:
         arg.append('-quiet')
     if not (nthreads is None):
         arg.extend(['-nthreads', str(nthreads)])
-    arg.extend([dim_str, size])
-    arg.extend(['-interp', interp])
-    arg.extend([input, output])
     completion = subprocess.run(arg)
     if completion.returncode != 0:
         raise Exception('Failed to reslice. See above for errors.')