Rename CWAS to MDMR

CPAC/GUI/interface/pages/__init__.py

@@ -12,7 +12,7 @@
 from .smoothing import AfterWarping, AfterWarpingOptions
 from .timeseries import TimeSeries, ROITimeseries
 from .group_analysis import GroupAnalysis, GPASettings, BASCSettings
-from .cwas import CWASSettings
+from .mdmr import MDMRSettings
 
 __all__ = [ 'SkullStripProcessing', 'SkullStripOptions', 'AFNI_options', 'BET_options',\
            'AnatomicalPreprocessing', 'Segmentation', \

CPAC/GUI/interface/pages/group_analysis.py

@@ -230,94 +230,3 @@ def __init__(self, parent, counter=0):
 
     def get_counter(self):
             return self.counter
-
-
-class CWAS(wx.html.HtmlWindow):
-    def __init__(self, parent, counter  = 0):
-        from urllib2 import urlopen
-        wx.html.HtmlWindow.__init__(self, parent, style= wx.html.HW_SCROLLBAR_AUTO)
-        self.SetStandardFonts()
-
-        self.counter = counter
-        self.LoadFile(p.resource_filename('CPAC', 'GUI/resources/html/cwas.html'))
-
-    def get_counter(self):
-        return self.counter
-
-
-class CWASSettings(wx.ScrolledWindow):
-
-    def __init__(self, parent, counter = 0):
-        wx.ScrolledWindow.__init__(self, parent)
-
-        self.counter = counter
-
-        self.page = GenericClass(self, "Connectome-wide Association Studies (CWAS)")
-
-        self.page.add(label="Run CWAS ", 
-                      control=control.CHOICE_BOX, 
-                      name='runCWAS', 
-                      type=dtype.LSTR, 
-                      comment="Run CWAS", 
-                      values=["Off","On"],
-                      wkf_switch = True)
-
-        self.page.add(label="CWAS ROI File ", 
-                     control=control.COMBO_BOX, 
-                     name='cwasROIFile', 
-                     type=dtype.STR, 
-                     values = "None",
-                     comment="Path to a mask file. Voxels outside this mask will be excluded from CWAS.")
-
-        self.page.add(label="CWAS Regressor File ", 
-                     control=control.COMBO_BOX, 
-                     name='cwasRegressorFile', 
-                     type=dtype.STR, 
-                     values= "None",
-                     comment = "Path to a text file containing phenotypic regressor.")
-
-        self.page.add(label= "CWAS FSamples ",
-                 control=control.INT_CTRL, 
-                 name='cwasFSamples', 
-                 type=dtype.NUM, 
-                 comment="Number of permutation tests to run on the Psuedo-F statistic.", 
-                 values=5000)
-
-        self.page.add(label= "CWAS Parallel Nodes ",
-                 control=control.INT_CTRL, 
-                 name='cwasParallelNodes', 
-                 type=dtype.NUM, 
-                 comment="Number of NiPype nodes to be created while computing CWAS.\n"\
-                         "This number depends on computing resources.", 
-                 values=10)
-
-        self.page.add(label= "Column Number with Regressor of Interest ",
-                 control=control.TEXT_BOX, 
-                 name='cwasRegressorCols', 
-                 type=dtype.LNUM, 
-                 values = "",
-                 size = (300,-1),
-                 validator = CharValidator("no-alpha"),
-                 comment="Column Number with Regressor of Interest.\n\nRemember this is 0 indexed so the 1st column is 0.\n\n"\
-                         "For instance, assuming the 1st column is the intercept, column number with regressor of interest = 1")
-
-        self.page.add(label= "CWAS Regressor Strata ",
-                 control=control.TEXT_BOX, 
-                 name='cwasRegressorStrata', 
-                 type=dtype.STR, 
-                 values = "None",
-                 size = (300,-1),
-                 comment="A list with length equal to the total number of rows in your regressor file.\n"\
-                         "Each element of the list, indicates that elements group. Leave it as None.\n"\
-                         "if you have a between-subject design and give it a value if not.\n"\
-                         "For instance, if you have multiple scans per subject, then you would want to\n"\
-                         "do a permutation within-subject between scans. For this to occur, the list\n"\
-                         "below could be something like ['s1', 's1', 's2', 's2', 's3', 's3', ...], \n"\
-                         "indicating what subject each element/scan is associated with and permutations"\
-                         "would only be done between scans within each subject.")
-
-        self.page.set_sizer()
-        parent.get_page_list().append(self)
-
-    def get_counter(self):
-            return self.counter

CPAC/GUI/interface/pages/cwas.py → CPAC/GUI/interface/pages/mdmr.py

@@ -5,51 +5,51 @@
 import os
 import pkg_resources as p
 
-class CWASSettings(wx.ScrolledWindow):
+class MDMRSettings(wx.ScrolledWindow):
     def __init__(self, parent, counter = 0):
         wx.ScrolledWindow.__init__(self, parent)
 
         self.counter = counter
 
-        self.page = GenericClass(self, "Connectome-wide Association Studies")
+        self.page = GenericClass(self, "Multivariate Distance Matrix Regression (MDMR)")
 
-        self.page.add(label="Run CWAS?",
+        self.page.add(label="Run MDMR?",
                       control=control.CHOICE_BOX,
-                      name="runCWAS",
+                      name="runMDMR",
                       type=dtype.LSTR,
-                      comment="Used to determine if Connectome-wide Association Studies "
+                      comment="Used to determine if Multivariate Distance Matrix Regression (MDMR) "
                               "will be added to the pipeline or not.",
                       values=["Off", "On"],
                       wkf_switch = True)
 
         self.page.add(label="Mask ROI File", 
                      control=control.COMBO_BOX,
-                     name='cwas_roi_file', 
+                     name='mdmr_roi_file', 
                      type=dtype.STR, 
                      values=str(""),
                      validation_req=False,
                      comment="Path to a mask file. Voxels outside of the mask will "
-                             "be excluded from CWAS.")
+                             "be excluded from MDMR.")
 
         self.page.add(label="Regressor file", 
                      control=control.COMBO_BOX,
-                     name="cwas_regressor_file", 
+                     name="mdmr_regressor_file", 
                      type=dtype.STR, 
                      values="",
                      comment="Path to a CSV file containing the phenotypic "
                              "regressor.")
 
         self.page.add(label="Regressor Participant Column Name",
                       control=control.TEXT_BOX,
-                      name="cwas_regressor_participant_column",
+                      name="mdmr_regressor_participant_column",
                       type=dtype.STR,
                       comment="Name of the participants column in your "
                               "regressor file.",
                       values="")
 
         self.page.add(label="Regressor of Interest columns", 
                      control=control.TEXT_BOX, 
-                     name="cwas_regressor_columns", 
+                     name="mdmr_regressor_columns", 
                      type=dtype.STR,
                      values="",
                      comment="Columns from the CSV file indicating factor "
@@ -58,18 +58,18 @@ def __init__(self, parent, counter = 0):
 
         self.page.add(label="Permutations",
                       control=control.INT_CTRL,
-                      name="cwas_permutations",
+                      name="mdmr_permutations",
                       type=dtype.NUM,
                       comment="Number of permutation tests to run on the "
                               "Pseudo-F statistics.",
                       values=500)
 
         self.page.add(label="Parallel nodes",
                       control=control.INT_CTRL,
-                      name="cwas_parallel_nodes",
+                      name="mdmr_parallel_nodes",
                       type=dtype.NUM,
                       comment="Number of Nipype nodes created while "
-                              "computing CWAS.  Dependent upon computing resources.",
+                              "computing MDMR. Dependent upon computing resources.",
                       values=1)
 
         self.page.set_sizer()

CPAC/GUI/interface/windows/config_window.py

@@ -14,7 +14,7 @@
     AfterWarping, AfterWarpingOptions,\
     FilteringSettings,\
     TimeSeries, EPI_DistCorr, ROITimeseries, \
-    GroupAnalysis, GPASettings, CWASSettings, TimeSeriesOptions, \
+    GroupAnalysis, GPASettings, MDMRSettings, TimeSeriesOptions, \
     BASCSettings
 
 ID_SUBMIT = 6
@@ -123,7 +123,7 @@ def __init__(self, parent):
         page45 = GroupAnalysis(self)
         page46 = GPASettings(self)
         page47 = BASCSettings(self)
-        page48 = CWASSettings(self)
+        page48 = MDMRSettings(self)
 
         # add the pages to the notebook with the label to show on the tab
         self.AddPage(page1, "Environment Setup", wx.ID_ANY)
@@ -177,7 +177,7 @@ def __init__(self, parent):
         self.AddSubPage(page46, "FSL FEAT Group Analysis", wx.ID_ANY)
         self.AddSubPage(page47, "Bootstrapped Analysis of Stable Clusters ",
                         wx.ID_ANY)
-        self.AddSubPage(page48, "CWAS Settings", wx.ID_ANY)
+        self.AddSubPage(page48, "MDMR Settings", wx.ID_ANY)
 
         self.Bind(wx.EVT_TREEBOOK_PAGE_CHANGED, self.OnPageChanged)
         self.Bind(wx.EVT_TREEBOOK_PAGE_CHANGING, self.OnPageChanging)

CPAC/GUI/resources/html/_sources/cwas.txt → CPAC/GUI/resources/html/_sources/mdmr.txt

@@ -1,4 +1,4 @@
-Connectome-wide Association Studies (CWAS)
+Multivariate Distance Matrix Regression (MDMR)
 ------------------------------------------
 
 Introduction & Background

CPAC/__main__.py

@@ -116,9 +116,9 @@ def quickrun(pipeline_dir, roi_file, roi_file_two=None, ref_file=None,
                                         basc_proc, basc_memory, scan=scan)
 
 
-@group.command(name="cwas")
+@group.command(name="mdmr")
 @click.argument("pipeline_config", type=click.Path(exists=True))
-def group_cwas(pipeline_config):
+def group_mdmr(pipeline_config):
     from CPAC.pipeline.cpac_group_runner import run_cwas
 
     run_cwas(pipeline_config)

CPAC/cwas/__init__.py

@@ -1,6 +1,6 @@
-from pipeline import joint_mask, \
-                 nifti_cwas, \
-                 create_cwas
+from .pipeline import joint_mask, \
+                      nifti_cwas, \
+                      create_cwas
 
 __all__ = ['create_cwas',
            'joint_mask',

CPAC/pipeline/cpac_group_runner.py

@@ -893,12 +893,12 @@ def run_cwas_group(output_dir, working_dir, roi_file,
     from CPAC.cwas.pipeline import create_cwas
 
     output_dir = os.path.abspath(output_dir)
-    working_dir = os.path.join(working_dir, 'group_analysis', 'CWAS',
+    working_dir = os.path.join(working_dir, 'group_analysis', 'MDMR',
                                os.path.basename(output_dir))
 
     inclusion_list = None
     if inclusion:
-        inclusion_list = load_text_file(inclusion, "CWAS participant "
+        inclusion_list = load_text_file(inclusion, "MDMR participant "
                                                    "inclusion list")
 
     output_df_dct = gather_outputs(output_dir,
@@ -931,7 +931,7 @@ def run_cwas_group(output_dir, working_dir, roi_file,
                 )
             }
 
-            cwas_wf = create_cwas(name="CWAS_{0}".format(df_scan))
+            cwas_wf = create_cwas(name="MDMR_{0}".format(df_scan))
             cwas_wf.inputs.inputspec.subjects = func_paths
             cwas_wf.inputs.inputspec.roi = roi_file
             cwas_wf.inputs.inputspec.regressor = regressor_file
@@ -955,13 +955,13 @@ def run_cwas(pipeline_config):
     output_dir = pipeconfig_dct["outputDirectory"]
     working_dir = pipeconfig_dct["workingDirectory"]
 
-    roi_file = pipeconfig_dct["cwas_roi_file"]
-    regressor_file = pipeconfig_dct["cwas_regressor_file"]
-    participant_column = pipeconfig_dct["cwas_regressor_participant_column"]
-    columns = pipeconfig_dct["cwas_regressor_columns"]
-    permutations = pipeconfig_dct["cwas_permutations"]
-    parallel_nodes = pipeconfig_dct["cwas_parallel_nodes"]
-    inclusion = pipeconfig_dct["cwas_inclusion"]
+    roi_file = pipeconfig_dct["mdmr_roi_file"]
+    regressor_file = pipeconfig_dct["mdmr_regressor_file"]
+    participant_column = pipeconfig_dct["mdmr_regressor_participant_column"]
+    columns = pipeconfig_dct["mdmr_regressor_columns"]
+    permutations = pipeconfig_dct["mdmr_permutations"]
+    parallel_nodes = pipeconfig_dct["mdmr_parallel_nodes"]
+    inclusion = pipeconfig_dct["mdmr_inclusion"]
 
     if not inclusion or "None" in inclusion or "none" in inclusion:
         inclusion = None

doc/workflows/index.rst

@@ -24,7 +24,7 @@ Contents:
     scrubbing
     group_analysis
     easy_thresh     
-    cwas
+    mdmr
     median_angle
     registration
     timeseries

doc/workflows/cwas.rst → doc/workflows/mdmr.rst

@@ -1,4 +1,4 @@
-Connectome Wide Association Studies
+Multivariate Distance Matrix Regression
 ===================================
 
 .. automodule:: CPAC.cwas