Fbudin at 19:24, 18 March 2016

2016-03-18T19:24:26Z

Fbudin at 19:21, 18 March 2016

2016-03-18T19:21:06Z

Fbudin: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 70: / Line 70: @@
 * Unbiased atlas creation
-    clean (boolean): Removes content of output directory before starting computation
+** clean (boolean): Removes content of output directory before starting computation
-    data_dir (string): directory containing 'file_list_file_name'
+** data_dir (string): directory containing 'file_list_file_name'
-    file_list_file_name (string): text file containing a list of image file paths, one per line
+** file_list_file_name (string): text file containing a list of image file paths, one per line
-    verbose (boolean): Displays more or less information while running
+** verbose (boolean): Displays more or less information while running
-    result_dir (string): output directory where outputs will be saved.
+** result_dir (string): output directory where outputs will be saved.
-    selection (list): select images that are processed in given list [must contain at least 2 values].
+** selection (list): select images that are processed in given list [must contain at least 2 values].
-    reference_im_fn (string): reference image used for the registration.
+** reference_im_fn (string): reference image used for the registration.
-    num_of_iterations_per_level (int): Number of iteration per level for the registration [>=0]
+** num_of_iterations_per_level (int): Number of iteration per level for the registration [>=0]
-    num_of_levels (int): Number of levels (starting the registration at a down-sampled level) for the registration [>=1]
+** num_of_levels (int): Number of levels (starting the registration at a down-sampled level) for the registration [>=1]
-    ants_params (see example and ANTS documentation):
+** ants_params (see example and ANTS documentation):
-    ants_params = {'Convergence' : '[100x50x25,1e-6,10]',\
+** number_of_cpu (integer/optional): Number of diffeomorphic registration run in parallel. In not specified, it will run as many processes as there are CPU available. Beware, the processes might already be multithreaded.
 * Low Rank/Sparse decomposition
-    clean (boolean): Removes content of output directory before starting computation
+** clean (boolean): Removes content of output directory before starting computation
-    data_dir (string): directory containing 'file_list_file_name'
+** data_dir (string): directory containing 'file_list_file_name'
-    file_list_file_name (string): text file containing a list of image file paths, one per line
+** file_list_file_name (string): text file containing a list of image file paths, one per line
-    verbose (boolean): Displays more or less information while running
+** verbose (boolean): Displays more or less information while running
-    lamda (float): the tuning parameter that weights between the low-rank component and the sparse component.
+** lamda (float): the tuning parameter that weights between the low-rank component and the sparse component.
-    sigma (float): blurring kernel size.
+** sigma (float): blurring kernel size.
-    result_dir (string): output directory where outputs will be saved.
+** result_dir (string): output directory where outputs will be saved.
-    selection (list): select images that are processed in given list [must contain at least 1 value].
+** selection (list): select images that are processed in given list [must contain at least 1 value].
-    reference_im_fn (string): reference image used for the registration.
+** reference_im_fn (string): reference image used for the registration.
-    registration (string): 'affine', 'rigid', or 'none'
+** registration (string): 'affine', 'rigid', or 'none'
-    histogram_matching (boolean/optional): If not specified or set to False, no histogram matching performed.
+** histogram_matching (boolean/optional): If not specified or set to False, no histogram matching performed.
 * Low Rank Atlas Creation
-    clean (boolean): Removes content of output directory before starting computation
+** clean (boolean): Removes content of output directory before starting computation
-    data_dir (string): directory containing 'file_list_file_name'
+** data_dir (string): directory containing 'file_list_file_name'
-    file_list_file_name (string): text file containing a list of image file paths, one per line
+** file_list_file_name (string): text file containing a list of image file paths, one per line
-    verbose (boolean): Displays more or less information while running
+** verbose (boolean): Displays more or less information while running
-    lamda (float): the tuning parameter that weights between the low-rank component and the sparse component.
+** lamda (float): the tuning parameter that weights between the low-rank component and the sparse component.
-    sigma (float): blurring kernel size.
+** sigma (float): blurring kernel size.
-    result_dir (string): output directory where outputs will be saved.
+** result_dir (string): output directory where outputs will be saved.
-    selection (list): select images that are processed in given list [must contain at least 2 values].
+** selection (list): select images that are processed in given list [must contain at least 2 values].
-    reference_im_fn (string): reference image used for the registration.
+** reference_im_fn (string): reference image used for the registration.
-    use_healthy_atlas (boolean): use a specified healthy atlas as reference image or compute a reference image from
+** use_healthy_atlas (boolean): use a specified healthy atlas as reference image or compute a reference image from the average of all the low-ranked images computed from the selected input images.
-                                 the average of all the low-ranked images computed from the selected input images.
+** num_of_iterations_per_level (int): Number of iteration per level for the registration [>=0]
-    num_of_iterations_per_level (int): Number of iteration per level for the registration [>=0]
+** num_of_levels (int): Number of levels (starting the registration at a down-sampled level) for the registration [>=1]
-    num_of_levels (int): Number of levels (starting the registration at a down-sampled level) for the registration [>=1]
+** registration_type (string): Type of registration performed, selected among [BSpline,ANTS,Demons]
-    registration_type (string): Type of registration performed, selected among [BSpline,ANTS,Demons]
+** ants_params (see example and ANTS documentation): Only necessary if registration_type is set to ANTS.
-    ants_params (see example and ANTS documentation): Only necessary if registration_type is set to ANTS.
+** number_of_cpu (integer/optional): Number of diffeomorphic registration run in parallel. In not specified, it will run as many processes as there are CPU available. Beware, the processes might already be multithreaded.
 * File List File Name: text file containing a list of image file paths, one per line
     /path/to/first/image.nrrd

@@ Line 69: / Line 69: @@
 {{documentation/{{documentation/version}}/module-section|Configuration files}}
-    Unbiased atlas creation
+* Unbiased atlas creation
      clean (boolean): Removes content of output directory before starting computation
      data_dir (string): directory containing 'file_list_file_name'
@@ Line 90: / Line 90: @@
                               already be multithreaded.
-    Low Rank/Sparse decomposition
+* Low Rank/Sparse decomposition
      clean (boolean): Removes content of output directory before starting computation
      data_dir (string): directory containing 'file_list_file_name'
@@ Line 103: / Line 103: @@
      histogram_matching (boolean/optional): If not specified or set to False, no histogram matching performed.
-    Low Rank Atlas Creation
+* Low Rank Atlas Creation
      clean (boolean): Removes content of output directory before starting computation
      data_dir (string): directory containing 'file_list_file_name'
@@ Line 128: / Line 128: @@
                               it will run as many processes as there are CPU available. Beware, the processes might
                               already be multithreaded.
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}

Documentation/Nightly/Extensions/pyLARSlicerExtension - Revision history

Fbudin at 19:24, 18 March 2016

Fbudin at 19:21, 18 March 2016

Fbudin: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}