Merge branch 'master' into afni_nwarpcat

Author: salma1601

CHANGES

@@ -1,10 +1,46 @@
-Upcoming release
+Upcoming release (0.14.0)
 ================
 
+* ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
 * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
 * ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
-* ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/#2203)
-* ENH: New ResourceMonitor - replaces resource profiler (https://github.com/nipy/nipype/pull/#2200)
+* ENH: Centralize virtual/physical $DISPLAYs (https://github.com/nipy/nipype/pull/2203, https://github.com/nipy/nipype/pull/2211)
+* ENH: New ResourceMonitor - replaces resource profiler (https://github.com/nipy/nipype/pull/2200)
+* ENH: Quickshear interface (https://github.com/nipy/nipype/pull/2047)
+* MAINT: updated deprecated HasTraits method (https://github.com/nipy/nipype/pull/2048)
+* ENH: CLI versioning (https://github.com/nipy/nipype/pull/2054)
+* ENH: Dual Regression interface (https://github.com/nipy/nipype/pull/2057)
+* ENH: Additional args to ANTs registration (https://github.com/nipy/nipype/pull/2062, https://github.com/nipy/nipype/pull/2078)
+* FIX: Mp2rage interfaces updated for new parameter names in cbstools 3 (https://github.com/nipy/nipype/pull/2065)
+* MAINT: Removed automatic nipype folder creation in HOME (https://github.com/nipy/nipype/pull/2076)
+* MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)
+* ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)
+* ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,
+       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, 
+       https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103,
+       https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186,
+       https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)
+* MAINT: cleanup and update AFNI's Allineate (https://github.com/nipy/nipype/pull/2098)
+* ENH: Add cosine-basis high-pass-filter to CompCor, allow skip of initial volumes (https://github.com/nipy/nipype/pull/2107, https://github.com/nipy/nipype/pull/#2122)
+* FIX: Catch more dcm2niix DTI conversions (https://github.com/nipy/nipype/pull/2110)
+* FIX: Retrieve aseg + wmparc stats properly (https://github.com/nipy/nipype/pull/2117)
+* ENH: ANTs MeasureImageSimilarity Inteface (https://github.com/nipy/nipype/pull/2128)
+* FIX: CompCor filter_basis of correct size, pre-filter column headers (https://github.com/nipy/nipype/pull/2136, https://github.com/nipy/nipype/pull/2138)
+* ENH: FreeSurfer lta_convert and mri_coreg interfaces (https://github.com/nipy/nipype/pull/2140, https://github.com/nipy/nipype/pull/2172)
+* ENH: Speed up S3DataGrabber (https://github.com/nipy/nipype/pull/2143)
+* FIX: Allow S3DataGrabber to grab single file (https://github.com/nipy/nipype/pull/2147)
+* FIX: Allow 4D images as inputs to buildtemplateparallel.sh and N4BiasFieldCorrection (https://github.com/nipy/nipype/pull/2151)
+* MAINT: Detect and warn unconnected duplicate nodes (https://github.com/nipy/nipype/pull/2163)
+* ENH: Calcmedian Interface (https://github.com/nipy/nipype/pull/2167)
+* FIX: probtrackx2 outputs (https://github.com/nipy/nipype/pull/2169)
+* ENH: Improve FreeSurfer registration (https://github.com/nipy/nipype/pull/2172)
+* ENH: BIDSDataGrabber interface (https://github.com/nipy/nipype/pull/2174)
+* MAINT: Set minimum numpy version to 1.9.0 (https://github.com/nipy/nipype/pull/2182)
+* ENH: Support for multiple intial-moving-transforms (https://github.com/nipy/nipype/pull/2187)
+* MAINT: Fixes for networkx and afni (https://github.com/nipy/nipype/pull/2196, https://github.com/nipy/nipype/pull/2171)
+* TST: Update C3D version in Docker build (https://github.com/nipy/nipype/pull/2199)
+* ENH: SimpleInterface interface (https://github.com/nipy/nipype/pull/2220)
+* ENH: Add LTA to Tkregister2 (https://github.com/nipy/nipype/pull/2217)
 
 0.13.1 (May 20, 2017)
 =====================

CODE_OF_CONDUCT.md

@@ -0,0 +1,73 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting project leaders Satrajit Ghosh <<satra@mit.edu>> or Chris Gorgolewski <<krzysztof.gorgolewski@gmail.com>>. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project leaders is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

CONTRIBUTING.md

@@ -1,3 +1,5 @@
+**Are you new to open source and GitHub?** If so reading the "[How to submit a contribution](https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution)" guide will provide a great introduction to contributing to Nipype and other Open Source projects. All the Nipype specific contributing instructions listed below will make much more sense after reading this guide.
+
 ## Contributing pull-requests (PRs)
 
 * All work is submitted via Pull Requests.
@@ -20,7 +22,7 @@
   * adding more information about what may have caused the error.
     Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
     Do not log this, as it creates redundant/confusing logs.
-* If you are new to the project don't forget to add your name and affiliation to the `.zenodo.json` file.
+* **If you are new to the project don't forget to add your name and affiliation to the `.zenodo.json` file.**
 
 ## Contributing issues
 

README.rst

@@ -90,33 +90,8 @@ To participate in the Nipype development related discussions please use the foll
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
+Contributing to the project
+---------------------------
 
-Nipype structure
-----------------
-
-Currently Nipype consists of the following files and directories:
-
-  INSTALL
-    NIPYPE prerequisites, installation, development, testing, and
-    troubleshooting.
-
-  README
-    This document.
-
-  THANKS
-    NIPYPE developers and contributors. Please keep it up to date!!
-
-  LICENSE
-    NIPYPE license terms.
-
-  doc/
-    Sphinx/reST documentation
-
-  examples/
-
-  nipype/
-    Contains the source code.
-
-  setup.py
-    Script for building and installing NIPYPE.
+If you'd like to contribute to the project please read our `guidelines <https://github.com/nipy/nipype/blob/master/CONTRIBUTING.md>`_. Please also read through our `code of conduct <https://github.com/nipy/nipype/blob/master/CODE_OF_CONDUCT.md>`_.
 

nipype/interfaces/afni/__init__.py

@@ -26,4 +26,4 @@
                     Refit, Resample, TCat, TCatSubBrick, TStat, To3D, Unifize,
                     Undump, ZCutUp, GCOR,
                     Zcat, Zeropad)
-from .model import (Deconvolve, Remlfit)
+from .model import (Deconvolve, Remlfit, Synthesize)

nipype/interfaces/afni/model.py

@@ -154,6 +154,12 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
     x1D_stop = traits.Bool(
         desc='stop running after writing .xmat.1D file',
         argstr='-x1D_stop')
+    cbucket = traits.Str(
+        desc='Name for dataset in which to save the regression '
+             'coefficients (no statistics). This dataset '
+             'will be used in a -xrestore run [not yet implemented] '
+             'instead of the bucket dataset, if possible.',
+        argstr='-cbucket %s')
     out_file = File(
         desc='output statistics file',
         argstr='-bucket %s')
@@ -231,6 +237,8 @@ class DeconvolveOutputSpec(TraitedSpec):
         desc='automatical generated script to run 3dREMLfit', exists=True)
     x1D = File(
         desc='save out X matrix', exists=True)
+    cbucket = File(
+        desc='output regression coefficients file (if generated)')
 
 
 class Deconvolve(AFNICommand):
@@ -588,3 +596,75 @@ def _list_outputs(self):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 
         return outputs
+
+
+class SynthesizeInputSpec(AFNICommandInputSpec):
+    cbucket = File(
+        desc='Read the dataset output from '
+             '3dDeconvolve via the \'-cbucket\' option.',
+        argstr='-cbucket %s',
+        copyfile=False,
+        mandatory=True)
+    matrix = File(
+        desc='Read the matrix output from '
+             '3dDeconvolve via the \'-x1D\' option.',
+        argstr='-matrix %s',
+        copyfile=False,
+        mandatory=True)
+    select = traits.List(
+        Str(desc='selected columns to synthesize'),
+        argstr='-select %s',
+        desc='A list of selected columns from the matrix (and the '
+             'corresponding coefficient sub-bricks from the '
+             'cbucket). Valid types include \'baseline\', '
+             ' \'polort\', \'allfunc\', \'allstim\', \'all\', '
+             'Can also provide \'something\' where something matches '
+             'a stim_label from 3dDeconvolve, and \'digits\' where digits '
+             'are the numbers of the select matrix columns by '
+             'numbers (starting at 0), or number ranges of the form '
+             '\'3..7\' and \'3-7\'.',
+        mandatory=True)
+    out_file = File(
+        name_template='syn',
+        desc='output dataset prefix name (default \'syn\')',
+        argstr='-prefix %s')
+    dry_run = traits.Bool(
+        desc='Don\'t compute the output, just '
+             'check the inputs.',
+        argstr='-dry')
+    TR = traits.Float(
+        desc='TR to set in the output.  The default value of '
+             'TR is read from the header of the matrix file.',
+        argstr='-TR %f')
+    cenfill = traits.Enum(
+        'zero','nbhr','none',
+        argstr='-cenfill %s',
+        desc='Determines how censored time points from the '
+             '3dDeconvolve run will be filled. Valid types '
+             'are \'zero\', \'nbhr\' and \'none\'.')
+
+
+class Synthesize(AFNICommand):
+    """Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve,
+       and synthesizes a fit dataset using user-selected sub-bricks and
+       matrix columns.
+
+    For complete details, see the `3dSynthesize Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSynthesize.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> synthesize = afni.Synthesize()
+    >>> synthesize.inputs.cbucket = 'functional.nii'
+    >>> synthesize.inputs.matrix = 'output.1D'
+    >>> synthesize.inputs.select = ['baseline']
+    >>> synthesize.cmdline  # doctest: +ALLOW_UNICODE
+    '3dSynthesize -cbucket functional.nii -matrix output.1D -select baseline'
+    >>> syn = synthesize.run()  # doctest: +SKIP
+    """
+
+    _cmd = '3dSynthesize'
+    input_spec = SynthesizeInputSpec
+    output_spec = AFNICommandOutputSpec

nipype/interfaces/afni/preprocess.py

@@ -15,7 +15,8 @@
 import os
 import os.path as op
 
-from ...utils.filemanip import (load_json, save_json, split_filename)
+from ...utils.filemanip import (load_json, save_json, split_filename,
+                                fname_presuffix)
 from ..base import (
     CommandLineInputSpec, CommandLine, TraitedSpec,
     traits, isdefined, File, InputMultiPath, Undefined, Str)
@@ -3131,7 +3132,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
              'Note that the source dataset in the second run is the SAME as'
              'in the first run.  If you don\'t see why this is necessary,'
              'then you probably need to seek help from an AFNI guru.',
-        argstr='-inlev %d',
+        argstr='-inilev %d',
         xor=['duplo'])
     minpatch = traits.Int(
         desc='* The value of mm should be an odd integer.'
@@ -3462,7 +3463,7 @@ class Qwarp(AFNICommand):
     >>> qwarp2.inputs.inilev = 7
     >>> qwarp2.inputs.iniwarp = ['Q25_warp+tlrc.HEAD']
     >>> qwarp2.cmdline  # doctest: +ALLOW_UNICODE
-    '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inlev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
+    '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
     >>> res2 = qwarp2.run()  # doctest: +SKIP
     """
     _cmd = '3dQwarp'
@@ -3475,29 +3476,38 @@ def _list_outputs(self):
         if not isdefined(self.inputs.out_file):
             prefix = self._gen_fname(self.inputs.in_file, suffix='_QW')
             ext = '.HEAD'
+            suffix ='+tlrc'
         else:
             prefix = self.inputs.out_file
             ext_ind = max([prefix.lower().rfind('.nii.gz'),
                            prefix.lower().rfind('.nii.')])
             if ext_ind == -1:
                 ext = '.HEAD'
+                suffix = '+tlrc'
             else:
                 ext = prefix[ext_ind:]
+                suffix = ''
         print(ext,"ext")
-        outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='+tlrc')+ext)
+        outputs['warped_source'] = fname_presuffix(prefix, suffix=suffix,
+                                                   use_ext=False) + ext
         if not self.inputs.nowarp:
-            outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARP+tlrc')+ext)
+            outputs['source_warp'] = fname_presuffix(prefix,
+                suffix='_WARP' + suffix, use_ext=False) + ext
         if self.inputs.iwarp:
-            outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_WARPINV+tlrc')+ext)
+            outputs['base_warp'] = fname_presuffix(prefix,
+                suffix='_WARPINV' + suffix, use_ext=False) + ext
         if isdefined(self.inputs.out_weight_file):
             outputs['weights'] = os.path.abspath(self.inputs.out_weight_file)
 
         if self.inputs.plusminus:
-            outputs['warped_source'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS+tlrc')+ext)
-            outputs['warped_base'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS+tlrc')+ext)
-            outputs['source_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_PLUS_WARP+tlrc')+ext)
-            outputs['base_warp'] = os.path.abspath(self._gen_fname(prefix, suffix='_MINUS_WARP+tlrc',)+ext)
-
+            outputs['warped_source'] = fname_presuffix(prefix,
+                suffix='_PLUS' + suffix, use_ext=False) + ext
+            outputs['warped_base'] = fname_presuffix(prefix,
+                suffix='_MINUS' + suffix, use_ext=False) + ext
+            outputs['source_warp'] = fname_presuffix(prefix,
+                suffix='_PLUS_WARP' + suffix, use_ext=False) + ext
+            outputs['base_warp'] = fname_presuffix(prefix,
+                suffix='_MINUS_WARP' + suffix, use_ext=False) + ext
         return outputs
 
     def _gen_filename(self, name):

nipype/interfaces/afni/tests/test_auto_Deconvolve.py

@@ -14,6 +14,8 @@ def test_Deconvolve_inputs():
     ),
     automask=dict(argstr='-automask',
     ),
+    cbucket=dict(argstr='-cbucket %s',
+    ),
     censor=dict(argstr='-censor %s',
     ),
     dmbase=dict(argstr='-dmbase',
@@ -127,7 +129,8 @@ def test_Deconvolve_inputs():
 
 
 def test_Deconvolve_outputs():
-    output_map = dict(out_file=dict(),
+    output_map = dict(cbucket=dict(),
+    out_file=dict(),
     reml_script=dict(),
     x1D=dict(),
     )

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -51,7 +51,7 @@ def test_Qwarp_inputs():
     copyfile=False,
     mandatory=True,
     ),
-    inilev=dict(argstr='-inlev %d',
+    inilev=dict(argstr='-inilev %d',
     xor=['duplo'],
     ),
     iniwarp=dict(argstr='-iniwarp %s',