change resolution_for_func to resolution_for_func_preproc in config

FCP-INDI · Aug 9, 2016 · e33cb53 · e33cb53
1 parent 4a4aae2
commit e33cb53
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Showing 5 changed files with 8 additions and 8 deletions.
diff --git a/CPAC/GUI/interface/pages/functional_tab.py b/CPAC/GUI/interface/pages/functional_tab.py
@@ -174,7 +174,7 @@ def __init__(self, parent, counter = 0):
 
         self.page.add(label="Functional Standard Resolution ", 
                      control=control.CHOICE_BOX, 
-                     name='resolution_for_func', 
+                     name='resolution_for_func_preproc', 
                      type=dtype.STR, 
                      values = ["3mm", "2mm", "1mm"],
                      comment="The resolution (in mm) to which functional images are transformed during registration")
@@ -183,14 +183,14 @@ def __init__(self, parent, counter = 0):
                       control=control.COMBO_BOX, 
                       name='template_brain_only_for_func', 
                       type=dtype.STR, 
-                      values = str(os.path.join(fsl,"data/standard/MNI152_T1_${resolution_for_func}_brain.nii.gz")),
+                      values = str(os.path.join(fsl,"data/standard/MNI152_T1_${resolution_for_func_preproc}_brain.nii.gz")),
                       comment="Standard FSL Skull Stripped Template. Used as a reference image for functional registration")
 
         self.page.add(label="Standard Template with Skull (functional resolution) ", 
                       control=control.COMBO_BOX, 
                       name='template_skull_for_func', 
                       type=dtype.STR, 
-                      values =  str(os.path.join(fsl,"data/standard/MNI152_T1_${resolution_for_func}.nii.gz")),
+                      values =  str(os.path.join(fsl,"data/standard/MNI152_T1_${resolution_for_func_preproc}.nii.gz")),
                       comment="Standard FSL Anatomical Brain Image with Skull")
 
         self.page.add(label="Standard Identity Matrix ", 

diff --git a/CPAC/GUI/resources/config_parameters.txt b/CPAC/GUI/resources/config_parameters.txt
@@ -46,7 +46,7 @@ func_reg_input,Use as Functional-to-Anatomical Registration Input,Functional to
 func_reg_input_volume,Functional Volume to Use as Input (Selected Functional Volume only),Functional to Anatomical Registration
 functionalMasking,Functional Masking,Functional to Anatomical Registration
 runRegisterFuncToMNI,Run Functional to MNI Registration,Functional to MNI Registration
-resolution_for_func,Functional Standard Resolution,Functional to MNI Registration
+resolution_for_func_preproc,Functional Standard Resolution,Functional to MNI Registration
 template_brain_only_for_func,Standard Brain only Template (functional resolution),Functional to MNI Registration
 template_skull_for_func,Standard Template with Skull (functional resolution),Functional to MNI Registration
 identityMatrix,Standard Identity Matrix,Functional to MNI Registration

diff --git a/CPAC/GUI/resources/html/_sources/func.txt b/CPAC/GUI/resources/html/_sources/func.txt
@@ -71,7 +71,7 @@ Configuration Using a YAML File
 To configure functional to MNI registration options within a YAML file, add the following lines to your file (with appropriate substitutions for paths)::
 
     runRegisterFuncToMNI : [1]
-    resolution_for_func : 2mm
+    resolution_for_func_preproc : 2mm
     template_brain_only_for_anat : /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
     template_skull_for_anat : /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
     identityMatrix : /usr/share/fsl/5.0/etc/flirtsch/ident.mat
diff --git a/benchmarks/sca_profiler.py b/benchmarks/sca_profiler.py
@@ -31,7 +31,7 @@ def get_workflow(c):
 
     """
     standard = os.path.join(c.FSLDIR,
-            'data/standard/MNI152_T1_%s.nii.gz' % (c.resolution_for_func))
+            'data/standard/MNI152_T1_%s.nii.gz' % (c.resolution_for_func_preproc))
 
     sca = None
     sca = create_sca(c.correlationSpace)

diff --git a/configs/pipeline_config.yml b/configs/pipeline_config.yml
@@ -278,11 +278,11 @@ resolution_for_func_derivatives :  2mm
 
 # Standard FSL Skull Stripped Template. Used as a reference image for functional
 # registration
-template_brain_only_for_func :  /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func}_brain.nii.gz
+template_brain_only_for_func :  /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func_preproc}_brain.nii.gz
 
 
 # Standard FSL Anatomical Brain Image with Skull
-template_skull_for_func :  /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func}.nii.gz
+template_skull_for_func :  /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_func_preproc}.nii.gz
 
 
 # Matrix containing all 1's. Used as an identity matrix during registration.