Merge branch 'enh/ImproveJSONInterfaces' into enh/AntsForFMBworkflow

Author: oesteban

CHANGES

@@ -5,51 +5,56 @@ Next release
        (https://github.com/nipy/nipype/pull/1019)
 * ENH: Improve JSON interfaces: default settings when reading and consistent output creation
        when writing (https://github.com/nipy/nipype/pull/1047)
+* FIX: Amend create_tbss_non_fa() workflow to match FSL's tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)
+* FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
+* ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
+* FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
 * ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
 * ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
 * BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
 * FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
 * ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
 * ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
-       New options also include choice of tracker, interpolator, stepsize and 
+       New options also include choice of tracker, interpolator, stepsize and
        curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
 * FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
 * FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
 * ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
-* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 
+* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
 	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
 	   (https://github.com/nipy/nipype/pull/990/files)
 * ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
 * FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
 * FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
 * ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
-* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is 
+* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
 	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
 * FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
 * FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
 * ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
 * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
+* ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
 
 Release 0.10.0 (October 10, 2014)
 ============
 
 * ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
        to enable parallel processing of very large images.
 * ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
-       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu 
+       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
        versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
 * ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
 * ENH: New dipy interfaces: Denoise, Resample
 * ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
 * ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
 * ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
-* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
        added to doctests, some bugs solved.
 * API: Interfaces to external packages are no longer available in the top-level
        ``nipype`` namespace, and must be imported directly (e.g.
        ``from nipype.interfaces import fsl``).
-* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
+* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
        AnalyzeWarp, PointsWarp, and EditTransform
 * ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
 * ENH: New Diffusion Toolkit interface: TrackMerge
@@ -65,7 +70,7 @@ Release 0.10.0 (October 10, 2014)
 * ENH: New color mode for write_graph
 * ENH: You can now force MapNodes to be run serially
 * ENH: Added ANTS based openfmri workflow
-* ENH: MapNode now supports flattening of nested lists 
+* ENH: MapNode now supports flattening of nested lists
 * ENH: Support for headless mode using Xvfb
 * ENH: nipype_display_crash has a debugging mode
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.

examples/fmri_ants_openfmri.py

@@ -218,7 +218,7 @@ def create_reg_workflow(name='registration'):
     reg.inputs.args = '--float'
     reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
     reg.inputs.num_threads = 4
-    reg.plugin_args = {'qsub_args': '-pe orte 4', 
+    reg.plugin_args = {'qsub_args': '-pe orte 4',
                        'sbatch_args': '--mem=6G -c 4'}
     register.connect(stripper, 'out_file', reg, 'moving_image')
     register.connect(inputnode,'target_image_brain', reg,'fixed_image')
@@ -428,7 +428,7 @@ def create_fs_reg_workflow(name='registration'):
     reg.inputs.args = '--float'
     reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
     reg.inputs.num_threads = 4
-    reg.plugin_args = {'qsub_args': '-pe orte 4', 
+    reg.plugin_args = {'qsub_args': '-pe orte 4',
                        'sbatch_args': '--mem=6G -c 4'}
     register.connect(stripper, 'out_file', reg, 'moving_image')
     register.connect(inputnode,'target_image', reg,'fixed_image')
@@ -562,17 +562,17 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id):
                                          'task%03d_run*' % (idx + 1))))
         runs = [int(val[-3:]) for val in files]
         run_ids.insert(idx, runs)
-    json_info = os.path.join(base_dir, subject_id, 'BOLD', 
-                                 'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]), 
+    json_info = os.path.join(base_dir, subject_id, 'BOLD',
+                                 'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]),
                                  'bold_scaninfo.json')
     if os.path.exists(json_info):
         import json
         with open(json_info, 'rt') as fp:
             data = json.load(fp)
             TR = data['global']['const']['RepetitionTime']/1000.
     else:
-        task_scan_key = os.path.join(base_dir, subject_id, 'BOLD', 
-                                 'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]), 
+        task_scan_key = os.path.join(base_dir, subject_id, 'BOLD',
+                                 'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]),
                                  'scan_key.txt')
         if os.path.exists(task_scan_key):
             TR = np.genfromtxt(task_scan_key)[1]
@@ -667,7 +667,7 @@ def analyze_openfmri_dataset(data_dir, subject=None, model_id=None,
                          name='datasource')
     datasource.inputs.base_directory = data_dir
     datasource.inputs.template = '*'
-    
+
     if has_contrast:
         datasource.inputs.field_template = {'anat': '%s/anatomy/T1_001.nii.gz',
                                             'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
@@ -909,18 +909,18 @@ def split_files(in_files, splits):
                splitfunc, 'in_files')
 
     if subjects_dir:
-        get_roi_mean = pe.MapNode(fs.SegStats(default_color_table=True), 
+        get_roi_mean = pe.MapNode(fs.SegStats(default_color_table=True),
                                   iterfield=['in_file'], name='get_aparc_means')
         get_roi_mean.inputs.avgwf_txt_file = True
         wf.connect(fixed_fx.get_node('outputspec'), 'copes', get_roi_mean, 'in_file')
         wf.connect(registration, 'outputspec.aparc', get_roi_mean, 'segmentation_file')
-        
-        get_roi_tsnr = pe.MapNode(fs.SegStats(default_color_table=True), 
+
+        get_roi_tsnr = pe.MapNode(fs.SegStats(default_color_table=True),
                                   iterfield=['in_file'], name='get_aparc_tsnr')
         get_roi_tsnr.inputs.avgwf_txt_file = True
         wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
         wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')
-        
+
     """
     Connect to a datasink
     """