feConnectomeSelectFibers

 Deletes a set of fibers from the signal and the M matrix.

   fe = feConnectomeSelectFibers(fe,fibersToKeep,[recomputeFibersInfo=0])

 The connectome select process builds the parameters inside of fe.life for
 a selected set of fibers.  The parameters inside of fe.life that are
 modified are

   The M matrix
   The fe.life.fibers entries

 We store and keep the whole connectome in .fg.  But not all calculations
 with the M matrix use all the fibers.  In some cases we run smaller
 subsets.

 Inputs:
   fe                  - an fe structure, see feCreate.m, and v_lifeExample.m
   fibersToKeep        - a list of indexes to the fibers to keep e.g., [1 10 100].
   recomputeFibersInfo - recomputes the fibers' info this takes a long time. 
                         So the default is not to recompute (0).

 Example:
   fibersToKeep = 1:50;
   feConnectomeSelectFibers(fe, fibersToKeep)

 See also:  fgExtract

 Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com.

0001 function fe = feConnectomeSelectFibers(fe, fibersToKeep,recomputeFibersInfo)
0002 % Deletes a set of fibers from the signal and the M matrix.
0003 %
0004 %   fe = feConnectomeSelectFibers(fe,fibersToKeep,[recomputeFibersInfo=0])
0005 %
0006 % The connectome select process builds the parameters inside of fe.life for
0007 % a selected set of fibers.  The parameters inside of fe.life that are
0008 % modified are
0009 %
0010 %   The M matrix
0011 %   The fe.life.fibers entries
0012 %
0013 % We store and keep the whole connectome in .fg.  But not all calculations
0014 % with the M matrix use all the fibers.  In some cases we run smaller
0015 % subsets.
0016 %
0017 % Inputs:
0018 %   fe                  - an fe structure, see feCreate.m, and v_lifeExample.m
0019 %   fibersToKeep        - a list of indexes to the fibers to keep e.g., [1 10 100].
0020 %   recomputeFibersInfo - recomputes the fibers' info this takes a long time.
0021 %                         So the default is not to recompute (0).
0022 %
0023 % Example:
0024 %   fibersToKeep = 1:50;
0025 %   feConnectomeSelectFibers(fe, fibersToKeep)
0026 %
0027 % See also:  fgExtract
0028 %
0029 % Copyright (2013-2014), Franco Pestilli, Stanford University, pestillifranco@gmail.com.
0030 
0031 if notDefined('recomputeFibersInfo'),recomputeFibersInfo=0;end
0032 fprintf('[%s], Selecting fibers from the full Connectome...\n',mfilename)
0033 
0034 % Change the name of the fe structure
0035 indx       = strfind(feGet(fe,'name'),'-');
0036 feFileName = feGet(fe,'name');
0037 if ~isempty(indx)
0038   feFileName = feFileName((indx(end) + 1):end); % Strip away any previous date-string tag.
0039 end
0040 feFileName = sprintf('%s-%s', datestr(now,30),feFileName);
0041 fe         = feSet(fe, 'name',feFileName);
0042 
0043 % Delete fibers' columns from the model.
0044 fe = feSet(fe,'Mfiber',feGet(fe,'mkeepfibers',fibersToKeep));
0045 
0046 % Remove the fibers from the fiber group:
0047 fe = feSet(fe,'fg',feGet(fe,'fiberssubset',fibersToKeep));
0048 
0049 % Take care of the field fe.life.fibers
0050 % Set the subset of tensors, the one only for the left-over fibers
0051 if ~isempty(fe.life.fibers.tensors)
0052   fe = feSet(fe,'tensors',feGet(fe,'tensors',fibersToKeep));
0053 end
0054 
0055 % Remove any fit or cross-validation
0056 fe = feSet(fe,'fit', []);
0057 fe = feSet(fe,'xvalfit',[]);
0058 
0059 % By default we do not recompute the fibers info.
0060 if recomputeFibersInfo
0061   % We disregard fibers that have identical trajectories within the ROI.
0062   roi = feGet(fe,'roi coords');
0063   fe  = feSet(fe,'voxel 2 fiber node pairs',fefgGet(feGet(fe,'fg'),'v2fn',roi));
0064   fe  = feGetConnectomeInfo(fe);
0065 else
0066   % this is done automatically by feSet:
0067   % fe = feSet(fe,'voxel 2 fiber node pairs',[]);
0068   fe = feSet(fe,'index to unique fibers in each voxel',[]);
0069   fe = feSet(fe,'number of unique fibers in each voxel', []);
0070   fe = feSet(fe,'number of total fibers in each voxel', []);
0071   fe = feSet(fe,'index of total fibers in each voxel', []);
0072 end
0073 
0074 return
0075