fix: resolved conflict

Author: satra

.travis.yml

@@ -3,10 +3,13 @@ python:
     - "2.7"
 before_install:
     - deactivate
+    - sudo rmdir /dev/shm
+    - sudo ln -Tsf /{run,dev}/shm
     - sudo apt-get update -qq
     - sudo apt-get install lsb-release
     - source /etc/lsb-release
-    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+    - echo ${DISTRIB_CODENAME}
+    - wget -O- http://neuro.debian.net/lists/${DISTRIB_CODENAME}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
     - sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
     - sudo apt-get update -qq
     - sudo apt-get install -qq python-scipy python-nose
@@ -18,4 +21,4 @@ before_install:
     - virtualenv --system-site-packages ~/virtualenv/this
     - source ~/virtualenv/this/bin/activate
 install: python setup.py build_ext --inplace
-script: make test
+script: make test

CHANGES

@@ -1,9 +1,20 @@
 Next release
 ============
-* ENH: New interfaces: nipy.Trim
 
+* ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss, spm.VBMSegment, fsl.InvWarp
 * ENH: Allow control over terminal output for commandline interfaces
 * ENH: Added preliminary support for generating Python code from Workflows.
+* ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction
+       with rotation of the B-matrix, and susceptibility correction for EPI imaging using
+       fieldmaps. Updated eddy_correct pipeline to support both dMRI and fMRI, and new parameters.
+* ENH: Minor improvements to FSL's FUGUE and FLIRT interfaces
+* ENH: Added optional dilation of parcels in cmtk.Parcellate 
+* ENH: Interpolation mode added to afni.Resample
+* ENH: Function interface can accept a list of strings containing import statements
+       that allow external functions to run without their imports defined in the
+       function body
+
+* FIX: SpecifyModel works with 3D files correctly now.
 
 Release 0.7.0 (Dec 18, 2012)
 ============================

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2006-2009, NIPY Developers
+Copyright (c) 2009-2013, NIPY Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -89,16 +89,13 @@ Currently NIPYPE consists of the following files and directories:
 License information
 -------------------
 
-See the file "LICENSE" for information on the history of this
-software, terms & conditions for usage, and a DISCLAIMER OF ALL
-WARRANTIES.
+We use the 3-clause BSD license; the full license is in the file ``LICENSE`` in
+the nipype distribution.
 
-This NIPYPE distribution contains no GNU General Public Licensed
-(GPLed) code so it may be used in proprietary projects.  There
-are interfaces to some GNU code but these are entirely optional.
+There are interfaces to some GNU code but these are entirely optional.
 
 All trademarks referenced herein are property of their respective
 holders.
 
-Copyright (c) 2009-2012, NIPY Developers
+Copyright (c) 2009-2013, NIPY Developers
 All rights reserved.

doc/users/function_interface.rst

@@ -71,6 +71,11 @@ be imported within the function itself::
 Without explicitly importing Nibabel in the body of the function, this
 would fail.
 
+Alternatively, it is possible to provide a list of strings corresponding
+to the imports needed to execute a function as a parameter of the `Function`
+constructor. This allows for the use of external functions that do not
+import all external definitions inside the function body.
+
 Hello World - Function interface in a workflow
 ----------------------------------------------
 

nipype/algorithms/modelgen.py

@@ -324,7 +324,12 @@ def _generate_standard_design(self, infolist,
             for i, out in enumerate(outliers):
                 numscans = 0
                 for f in filename_to_list(sessinfo[i]['scans']):
-                    numscans += load(f).get_shape()[3]
+                    shape = load(f).get_shape()
+                    if len(shape) == 3 or shape[3] == 1:
+                        iflogger.warning("You are using 3D instead of 4D files. Are you sure this was intended?")
+                        numscans += 1
+                    else:
+                        numscans += shape[3]
                 for j, scanno in enumerate(out):
                     colidx = len(sessinfo[i]['regress'])
                     sessinfo[i]['regress'].insert(colidx, dict(name='', val=[]))

nipype/interfaces/afni/__init__.py

@@ -11,4 +11,5 @@
 from .preprocess import (To3D, Refit, Resample, TStat, Automask, Volreg, Merge,
                          ZCutUp, Calc, TShift, Warp, Detrend, Despike, Copy,
                          Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
-                         TCorrelate, BrickStat, ROIStats, AutoTcorrelate)
+                         TCorrelate, BrickStat, ROIStats, AutoTcorrelate,
+                         BlurInMask, Autobox, TCorrMap, Bandpass)

nipype/interfaces/afni/base.py

@@ -135,7 +135,7 @@ def _output_update(self):
         self._outputtype = self.inputs.outputtype
 
     @classmethod
-    def set_default_outputtype(cls, outputtype):
+    def set_default_output_type(cls, outputtype):
         """Set the default output type for AFNI classes.
 
         This method is used to set the default output type for all afni
@@ -216,9 +216,10 @@ def _gen_filename(self, name):
 
             _, base, _ = split_filename(
                 getattr(self.inputs, trait_spec.name_source))
-            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd='')
+            return self._gen_fname(basename=base, prefix=prefix, suffix=suffix, cwd=os.getcwd())
         else:
-            return super(AFNICommand, self)._gen_filename(name)
+            return os.path.join(os.getcwd(),
+                                super(AFNICommand, self)._gen_filename(name))
 
     def _overload_extension(self, value):
         path, base, _ = split_filename(value)
@@ -231,7 +232,8 @@ def _list_outputs(self):
             outputs = self.output_spec().get()
             for name in out_names:
                 out = self._gen_filename(name)
-                outputs[name] = os.path.abspath(out)
+                if isdefined(out):
+                    outputs[name] = os.path.abspath(out)
             return outputs