anishas latest changes

Author: akeshavan

bips/workflows/__init__.py

@@ -14,6 +14,9 @@
 import synced_corr_display_h5
 import workflow14
 import workflow15
+import workflow16
+import workflow17
+import workflow18
 
 from .base import (list_workflows, configure_workflow, run_workflow,
                    display_workflow_info)

bips/workflows/scripts/u0a14c5b5899911e1bca80023dfa375f2/base.py

@@ -181,7 +181,8 @@ def create_prep(name='preproc'):
                                                       'filter_type',
                                                       'timepoints_to_remove',
                                                       'do_whitening',
-                                                      'regress_before_PCA']),
+                                                      'regress_before_PCA',
+                                                      'nipy_realign_parameters']),
                         name='inputspec')
 
     # Separate input node for FWHM
@@ -204,7 +205,8 @@ def create_prep(name='preproc'):
     #motion_correct = pe.Node(interface=FmriRealign4d(),
     #                            name='realign')
 
-    motion_correct = pe.Node(util.Function(input_names=['node','in_file','tr','do_slicetime','sliceorder'],
+    motion_correct = pe.Node(util.Function(input_names=['node','in_file','tr',
+                                                        'do_slicetime','sliceorder',"nipy_dict"],
         output_names=['out_file','par_file'],
         function=mod_realign),
         name="mod_realign")
@@ -291,6 +293,8 @@ def create_prep(name='preproc'):
                     ad, 'zintensity_threshold')
     preproc.connect(inputnode, 'tr',
                     motion_correct, 'tr')
+    preproc.connect(inputnode, 'nipy_realign_parameters',
+        motion_correct, 'nipy_dict')
     preproc.connect(inputnode, 'do_slicetime',
                     motion_correct, 'do_slicetime')
     preproc.connect(inputnode, 'sliceorder',

bips/workflows/scripts/u0a14c5b5899911e1bca80023dfa375f2/modular_nodes.py

@@ -3,7 +3,8 @@
 import nipype.interfaces.fsl as fsl
 
 
-def mod_realign(node,in_file,tr,do_slicetime,sliceorder):
+def mod_realign(node,in_file,tr,do_slicetime,sliceorder,
+                nipy_dict={"loops": 5, "speedup": 5, "between_loops":None}):
     import nipype.interfaces.fsl as fsl
     import nipype.interfaces.spm as spm
     import nipype.interfaces.nipy as nipy
@@ -13,12 +14,12 @@ def mod_realign(node,in_file,tr,do_slicetime,sliceorder):
         realign = nipy.FmriRealign4d()
         realign.inputs.in_file = in_file
         realign.inputs.tr = tr
-        realign.inputs.interleaved= False
+        realign.inputs.loops = nipy_dict["loops"]
+        realign.inputs.speedup = nipy_dict["speedup"]
+        realign.inputs.between_loops = nipy_dict["between_loops"]
         if do_slicetime:
             realign.inputs.slice_order = sliceorder
-        else:
-            realign.inputs.time_interp = False
-            realign.inputs.slice_order = [0]
+            realign.inputs.time_interp = True
 
         res = realign.run()
         out_file = res.outputs.out_file

bips/workflows/workflow1.py

@@ -75,7 +75,9 @@ class config(HasTraits):
     motion_correct_node = traits.Enum('nipy','fsl','spm','afni',
                                       desc="motion correction algorithm to use",
                                       usedefault=True,)
-    
+    loops = traits.List([5],traits.Int(5),usedefault=True)
+    #between_loops = traits.Either("None",traits.List([5]),usedefault=True)
+    speedup = traits.List([5],traits.Int(5),usedefault=True)
     # Artifact Detection
 
     norm_thresh = traits.Float(1, min=0, usedefault=True, desc="norm thresh for art")
@@ -222,6 +224,10 @@ def prep_workflow(c, fieldmap):
         preproc.remove_nodes([z_score])
 
     preproc.inputs.inputspec.motion_correct_node = c.motion_correct_node
+
+    preproc.inputs.inputspec.nipy_realign_parameters = {"loops":c.loops,
+                                                        "between_loops":None,
+                                                        "speedup":c.speedup}
     preproc.inputs.inputspec.timepoints_to_remove = c.timepoints_to_remove
     preproc.inputs.inputspec.smooth_type = c.smooth_type
     preproc.inputs.inputspec.surface_fwhm = c.surface_fwhm
@@ -364,6 +370,9 @@ def create_view():
                       Item(name='TR'),
                       Item(name='do_slicetiming'),
                       Item(name='SliceOrder', editor=CSVListEditor()),
+                      Item(name='loops',enabled_when="motion_correct_node=='nipy' ", editor=CSVListEditor()),
+                      #Item(name='between_loops',enabled_when="motion_correct_node=='nipy' "),
+                      Item(name='speedup',enabled_when="motion_correct_node=='nipy' ", editor=CSVListEditor()),
                       label='Motion Correction', show_border=True),
                 Group(Item(name='norm_thresh'),
                       Item(name='z_thresh'),

bips/workflows/workflow2.py

@@ -248,6 +248,8 @@ def create_view():
                       Item(name='TR'),
                       Item(name='do_slicetiming'),
                       Item(name='SliceOrder',editor=CSVListEditor()),
+                      Item(name='loops',enabled_when="motion_correct_node=='nipy' ", editor=CSVListEditor()),
+                      Item(name='speedup',enabled_when="motion_correct_node=='nipy' ", editor=CSVListEditor()),
                       label='Motion Correction', show_border=True),
                 Group(Item(name='norm_thresh'),
                       Item(name='z_thresh'),

bips/workflows/workflow3.py

@@ -82,7 +82,7 @@ def preproc_datagrabber(c,name='preproc_datagrabber'):
                                             tsnr_stddev='%s/preproc/tsnr/*tsnr_stddev.nii*',
                                             reg_file='%s/preproc/bbreg/*.dat',
                                             mean_image='%s/preproc/mean*/*.nii*',
-                                            mask='%s/preproc/mask/*_brainmask.nii')
+                                            mask='%s/preproc/mask/*/*.nii*')
     datasource.inputs.template_args = dict(motion_parameters=[['subject_id']],
                                            outlier_files=[['subject_id']],
                                            art_norm=[['subject_id']],
@@ -97,7 +97,7 @@ def preproc_datagrabber(c,name='preproc_datagrabber'):
     return datasource
 
 
-def start_config_table(c):
+def start_config_table(c,c_qa):
     table = []
     table.append(['TR',str(c.TR)])
     table.append(['Slice Order',str(c.SliceOrder)])
@@ -110,9 +110,9 @@ def start_config_table(c):
     table.append(['Art: z thresh',str(c.z_thresh)])
     #table.append(['Smoothing Algorithm',c.smooth_type])
     table.append(['fwhm',str(c.fwhm)])
-    if c.task:
+    if c_qa.task:
         table.append(['Highpass cutoff',str(c.hpcutoff)])
-    if c.resting:
+    if c_qa.resting:
         table.append(['highpass freq',str(c.highpass_freq)])
         table.append(['lowpass freq',str(c.lowpass_freq)])
     return table
@@ -371,8 +371,8 @@ def main(config_file):
     if QA_config.test_mode:
         a.write_graph()
 
-    a.inputs.inputspec.config_params = start_config_table(c)
-    a.config = {'execution' : {'crashdump_dir' : QA_config.crash_dir}}
+    a.inputs.inputspec.config_params = start_config_table(c,QA_config)
+    a.config = {'execution' : {'crashdump_dir' : QA_config.crash_dir, 'job_finished_timeout' : 14}}
 
     if QA_config.use_advanced_options:
         exec QA_config.advanced_script

example_configs/config.py

@@ -23,7 +23,7 @@
 
 After running preprocessing, you can run the first level pipeline:
 
-python first_level.py
+python workflow10.py
 
 
 Directories: