Table of Contents
NeuroElf Resources
Online resources
http://neuroelf.net/wiki/doku.php
https://www.youtube.com/channel/UC1sM-zqnmdcZOrRf-i0FLGg | NeuroElf youtube tutorials!
Help
For getting detailed help on each method of xff object (e.g. fmr), use:
>> fmr.Help % to see all methods >> fmr.Help('Method') % e.g. fmr.Help('Realign') to see details of each method
NeuroElf-based ERA
DAG installation notes
1) During installation, disable (remove from path) Chronux (if present): conflict with linec.m
2) NeuroElf functions use std.m and var.m as in newer versions of MATLAB, with 3 inputs: e.g. Y = STD(X,FLAG,DIM). Therefore, old NaN toolbox functions std.m and var.m were incompatible and sterr.m was updated. The old version of std.m is now available as ig_std.m in Igtools (corrcoef_eval.m has not been revised yet but is not needed for running the pipeline).
3) Starting from NeuroElf_v09d, many useful auxiliary scripts/functions are “hidden” behind @neuroelf method, and reside in ..\@neuroelf\private. They can be placed in the path (i.e. copied to the main NeuroElf folder, it is not possible to add to path this private folder directly), or accessed as described in [main installation folder] / README.html > Function library:
>> netools = neuroelf; >> list_of_files = netools.findfiles(startfolder, pattern);
The functions below should be in the NeuroElf base (root) folder (e.g. D:\Sources\NeuroElf_v10_4503). Only this folder should be on the path!
4) There is a bug in NeuroElf v1.0 and v0.9d, to fix please replace the function dcm_Value.m in /xff/private with the function below. This function is used by createfmr.m
- dcm_Value.m
function dcmval = dcm_Value(hfile, vkey, varargin) % DCM::Value - return a tag's value % % FORMAT: dcmval = dcm.Value(key [, ...]); % % Input fields: % % key DICOM key (0008.0010) or tag (PatientsName) % ... default value if not found % % Output fields: % % dcmval value for given key/tag % % Using: makelabel, splittocell. % Version: v0.9d % Build: 14082218 % Date: Aug-22 2014, 6:14 PM EST % Author: Jochen Weber, SCAN Unit, Columbia University, NYC, NY, USA % URL/Info: http://neuroelf.net/ % % Copyright (c) 2010, 2011, 2014, Jochen Weber % All rights reserved. % % Redistribution and use in source and binary forms, with or without % modification, are permitted provided that the following conditions are met: % * Redistributions of source code must retain the above copyright % notice, this list of conditions and the following disclaimer. % * Redistributions in binary form must reproduce the above copyright % notice, this list of conditions and the following disclaimer in the % documentation and/or other materials provided with the distribution. % * Neither the name of Columbia University nor the % names of its contributors may be used to endorse or promote products % derived from this software without specific prior written permission. % % THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND % ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED % WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE % DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY % DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES % (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; % LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND % ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT % (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS % SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. % neuroelf library global ne_methods; % persistent dictionaries persistent dcmv_dicts if isempty(dcmv_dicts) dcmv_dicts = struct; % load standard dict dcmv_dicts.OFFIS = ne_methods.dicom_dic(); % IK added ne_methods and () end % only valid for single file if nargin < 2 || ... numel(hfile) ~= 1 || ... ~xffisobject(hfile, true, 'dcm') error( ... 'xff:BadArgument', ... 'Invalid call to %s.', ... mfilename ... ); end % dict bc = xffgetcont(hfile.L); dict = bc.DataDictionary; % check key if ischar(vkey) vkey = vkey(:)'; if length(vkey) == 9 && ... ~isempty(regexpi(vkey, '^[0-9a-f]{4}[^0-9a-f][0-9a-f]{4}$')) vkey = vkey([1:4,6:9]); end if length(vkey) == 8 && ... ~isempty(regexpi(vkey, '^[0-9a-f]+$')) && ... ~all(double(vkey) > 64) vkey = ['k_' upper(vkey(1:4)) '_' upper(vkey(5:8))]; elseif ~strcmp(vkey, ne_methods.makelabel(vkey)) error( ... 'xff:BadArgument', ... 'Invalid DICOM tag number/key given.' ... ); else if isempty(dict) warning( ... 'xff:InternalWarning', ... 'Data dictionary not looked up.' ... ); dcm_DetectDictionary(hfile, 'auto'); dict = bc.DataDictionary; end if ~isfield(dcmv_dicts, dict) error( ... 'xff:BadSetting', ... 'Unknown DICOM dictionary set.' ... ); end dict = dcmv_dicts.(dict); if ~isfield(dict, vkey) error( ... 'xff:BadArgument', ... 'Unknown DICOM tag key given.' ... ); end vkey = dict.(vkey); if isfield(bc.DataKeyLookup, vkey) dcmval = bc.Data(bc.DataKeyLookup.(vkey)).Value; elseif isfield(bc.MetaKeyLookup, vkey) dcmval = bc.Meta(bc.MetaKeyLookup.(vkey)).Value; elseif nargin > 2 dcmval = varargin{1}; else error( ... 'xff:BadArgument', ... 'Given DICOM tag key not present in file.' ... ); end dcmval = interpret_dcmval(dcmval); return; end if ~isfield(bc.DataKeyLookup, vkey) if nargin < 3 error( ... 'xff:BadArgument', ... 'Given DICOM tag not present in file.' ... ); else dcmval = varargin{1}; dcmval = interpret_dcmval(dcmval); return; end end dcmval = bc.Data(bc.DataKeyLookup.(vkey)).Value; dcmval = interpret_dcmval(dcmval); % numeric key format elseif isa(vkey, 'double') if numel(vkey) == 2 && ... ~any(isinf(vkey) | isnan(vkey) | vkey < 0 | vkey > 65535) try dcmval = dcm_Value(hfile, sprintf('%04x%04x', vkey(1), vkey(2)), varargin{:}); catch ne_eo; rethrow(ne_eo); end elseif numel(vkey) == 1 && ... nargin > 2 && ... isa(varargin{1}, 'double') && ... ~isinf(vkey) && ... ~isnan(vkey) && ... vkey >= 0 && ... vkey < 65536 && ... numel(varargin{1}) == 1 && ... ~isinf(varargin{1}) && ... ~isnan(varargin{1}) && ... varargin{1} >= 0 && ... varargin{1} < 65536 try dcmval = dcm_Value(hfile, sprintf('%04x%04x', vkey, varargin{1}), varargin{2:end}); catch ne_eo; rethrow(ne_eo); end else error( ... 'xff:BadArgument', ... 'Invalid DICOM tag (or key) given.' ... ); end dcmval = interpret_dcmval(dcmval); else error( ... 'xff:BadArgument', ... 'Invalid DICOM tag (or key) given.' ... ); end % sub function function dcmval = interpret_dcmval(dcmval) global ne_methods; if ischar(dcmval) && ... ~isempty(dcmval) dcmval = dcmval(:)'; if ~isempty(regexpi(dcmval, ... '^\s*[\+\-]?\d+(\.\d+)?([eE][\+\-]?\d+)?(\s*\\\s*[\+\-]?\d+(\.\d+)?([eE][\+\-]?\d+)?)*\s*$')) dcmvalc = ne_methods.splittocell(dcmval, '\'); dcmvaln = zeros(1, numel(dcmvalc)); try for vc = 1:numel(dcmvalc) dcmvaln(vc) = str2double(dcmvalc{vc}); end catch ne_eo; neuroelf_lasterr(ne_eo); return; end dcmval = dcmvaln; end elseif isnumeric(dcmval) dcmval = double(dcmval); end % end of function dcmval = interpret_dcmval(dcmval)