Segment a fascicle from a connectome by applying a series of 'AND' and
'NOT' operations between the connectome and a set of ROIs.
The important aspect of this function is that it returns both the new
fiber group AND the indices in the origianl fiber group of the fibers
that passed all the 'and' and 'not' operations requested.
These idices can be used to address the columns of a LiFE model (M
matrix). This allows for subtracting entire fiber group dfined
anatomically from a pre-existing connectome. In turns this allows for
testing hypotheses on the improtance of an (anatomically selected)
fascicle within the volume of white-mater comprised by the connectome.
[fg fibersIndices] = feSegmentFascicleFromConnectome(fg, rois, operation, fascicleFileName)
INPUTS:
fg - A connectome (e.g., fg = feGet(fe,'fibers acpc'))
rois - A cell array of rois to be used for selecting the fibers in the
final fascicle
operation - A set of logical operations to be applied to the fibers in
the connectome in relation to the rois. There should be one
operation per roi.
fascicleName - The name of the final fascicle.
OUTPUTS:
fg - The segmented fiber group, containing only the fibers
that passed all the logical operations.
keepFG - A vector of indices (0's and 1's) of the length of the
number of fibers in the input fiber group. A one
indicates that the fiber survived all the logical
operations requested. A 0 indicates that the fibers did
not survive some of the logical operations and it was
deleted from the output fiber group.
Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com.0001 function [fg, keepFG] = feSegmentFascicleFromConnectome(fg, rois, operation, fascicleFileName) 0002 % Segment a fascicle from a connectome by applying a series of 'AND' and 0003 % 'NOT' operations between the connectome and a set of ROIs. 0004 % 0005 % The important aspect of this function is that it returns both the new 0006 % fiber group AND the indices in the origianl fiber group of the fibers 0007 % that passed all the 'and' and 'not' operations requested. 0008 % 0009 % These idices can be used to address the columns of a LiFE model (M 0010 % matrix). This allows for subtracting entire fiber group dfined 0011 % anatomically from a pre-existing connectome. In turns this allows for 0012 % testing hypotheses on the improtance of an (anatomically selected) 0013 % fascicle within the volume of white-mater comprised by the connectome. 0014 % 0015 % [fg fibersIndices] = feSegmentFascicleFromConnectome(fg, rois, operation, fascicleFileName) 0016 % 0017 % INPUTS: 0018 % fg - A connectome (e.g., fg = feGet(fe,'fibers acpc')) 0019 % rois - A cell array of rois to be used for selecting the fibers in the 0020 % final fascicle 0021 % operation - A set of logical operations to be applied to the fibers in 0022 % the connectome in relation to the rois. There should be one 0023 % operation per roi. 0024 % fascicleName - The name of the final fascicle. 0025 % 0026 % 0027 % OUTPUTS: 0028 % fg - The segmented fiber group, containing only the fibers 0029 % that passed all the logical operations. 0030 % keepFG - A vector of indices (0's and 1's) of the length of the 0031 % number of fibers in the input fiber group. A one 0032 % indicates that the fiber survived all the logical 0033 % operations requested. A 0 indicates that the fibers did 0034 % not survive some of the logical operations and it was 0035 % deleted from the output fiber group. 0036 % 0037 % Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com. 0038 0039 % Make sure that the inputs have one logical operation per ROI 0040 if ~(length(rois) == length(operation)) 0041 error('[%s] Please provide one logical operand (e.g., ''and'', ''not'') for each ROI...',mfilename) 0042 end 0043 0044 % Read fibers, if a path was passed 0045 if ~isstruct(fg) 0046 fg = fgRead(fg); 0047 end 0048 0049 % The following is the vector containing the indices 0050 % to the fibers we KEEP from the origianl fiber group 0051 % after all the logical operations are applied. 0052 keepFG = false(length(fg.fibers),1); 0053 0054 % The following is a cell array which will old the relative indices of the 0055 % fibers into each sized-down version of the fibers. 0056 % Each entry of the cell arry holds the indices to the fibergroup in the 0057 % before the current operation was applied. 0058 currentFibIndices = cell(length(rois)+1,1); 0059 currentFibIndices{1} = 1:length(keepFG); 0060 0061 for ir = 1:length(rois) 0062 % Read the rois from disk if paths were passed in 0063 if ~isstruct(rois{ir}) 0064 rois{ir} = dtiReadRoi(rois{ir}); 0065 end 0066 0067 % Intersect the wholebrain fiber group with "AND" / "NOT" ROIs 0068 [fg, ~, keep] = dtiIntersectFibersWithRoi([],operation{ir},[],rois{ir},fg); 0069 0070 % Select the indices fo the fibers that were deleted in the previous 0071 % loop. The way we address these indices depends on the type of operation. 0072 % For 'and' we simply use the idices in keep{ir-1} 0073 % For 'not' we need to flip the sign and use the indices in kee{ir-1} 0074 % that were se to 0. 0075 % 0076 % See help dtiIntersectFibersWithRoi.m 0077 % "The output variables keep and keepID vectors for "not" option are 0078 % counterintuitive: they mark fibers that DO intersect the ROI and that are 0079 % exluded from the output FG." 0080 switch operation{ir} 0081 case {'and','AND','and both endpoints','endpoints'} 0082 currentFibIndices{ir+1} = currentFibIndices{ir}(keep); 0083 case {'not','NOT'} 0084 currentFibIndices{ir+1} = currentFibIndices{ir}(~keep); 0085 otherwise 0086 keyboard 0087 end 0088 clear keep 0089 end 0090 0091 % Save the indices of the fibers that survived all the operations. 0092 keepFG( currentFibIndices{end} ) = true; 0093 0094 % Clean up the rest of the fields in the fiber group. 0095 % dtiIntersectFibersWithRoi.m does not handle other fields but the .fiber 0096 % one. 0097 fg.pathwayInfo = []; 0098 fg.seeds = []; 0099 fg.Q = []; 0100 fg.params = []; 0101 0102 % Change the fibergroup name 0103 if isstruct(fascicleFileName) 0104 fg.name = fascicleFileName.name; 0105 else 0106 fg.name = fascicleFileName; 0107 end 0108 return