From 72bfc1606dd98f4d1e5d37b92bb0f5870c6505ba Mon Sep 17 00:00:00 2001
From: Mathieu Boudreau <emb6150@gmail.com>
Date: Wed, 24 Aug 2022 14:09:20 -0300
Subject: [PATCH] Add nofilter script

---
 cneuromod/nofilter_map_neuromod.m | 173 ++++++++++++++++++++++++++++++
 1 file changed, 173 insertions(+)
 create mode 100644 cneuromod/nofilter_map_neuromod.m

diff --git a/cneuromod/nofilter_map_neuromod.m b/cneuromod/nofilter_map_neuromod.m
new file mode 100644
index 0000000..52d1235
--- /dev/null
+++ b/cneuromod/nofilter_map_neuromod.m
@@ -0,0 +1,173 @@
+% Simple wrapper for filtering B1plus maps
+%
+% Required inputs:
+%
+%    Image file names:
+%        - b1plus_nii --> subID*.nii.gz (e.g. sub-01_B1plusmap.nii.gz)
+%
+% filter_map_wrapper(___,PARAM1, VAL1, PARAM2, VAL2,___)
+%
+% Parameters include:
+%
+%   'mask'              File name for the (.nii.gz formatted)
+%                       binary mask. (stiring)
+%
+%   'siemens'           Indicates whether the raw B1map is acquired using 
+%                       Siemens TFL B1map sequence. If so, the map 
+%                       will be divided by 800. (boolean)
+%
+%   'type'              Type of filter (string)
+%                           - 'gaussian'
+%                           - 'median'
+%                           - 'spline'
+%                           - 'polynomial'
+%
+%   'dimension'         In which dimensions to apply the filter (string)
+%                           - '2D'
+%                           - '3D'
+%
+%   'order'             Depends on the type selection (integer)
+%                           - For type polynomial, it is the order of the polynomial.
+%                           - For type spline, it is the 'amount of smoothness'
+%
+%   'size'              Extent of filter in number of voxels (x y z) (vector)
+%                           - For type gaussian, it is FWHM.
+%                           - For type median, it is number of voxels.
+%       
+%   'qmrlab_path'       Absolute path to the qMRLab's root directory. (string)
+% 
+% Outputs: 
+%
+%    subID_B1plusmap_filtered.nii.gz       Filtered B1 plus map. 
+%
+%    subID_B1plusmap_filtered.json         Filtered B1 plus map metadata. 
+%                                          
+%    subID_filter_map_qmrlab.mat  Object containing qMRLab options. 
+% 
+% IMPORTANT:
+%
+%    FitResults.mat     Removed after fitting.
+%
+%    Subject ID         This wrapper assumes that the input data
+%                       has a subject ID prefix before the first
+%                       occurence of the '_' character.  
+%
+% Written by: Agah Karakuzu, 2020
+% GitHub:     @agahkarakuzu
+%
+% Intended use: qMRFlow 
+% =========================================================================
+
+
+function nofilter_map_neuromod(SID,b1plus_nii,varargin)
+
+    disp('Runnning filtermap neuromod latest');
+
+    if moxunit_util_platform_is_octave
+       warning('off','all');
+    end
+    
+    validDir = @(x) exist(x,'dir');
+    
+    keyval = regexp(SID,'[^-_]*','match');
+    
+    p = inputParser();
+    
+    %Input parameters conditions
+    validNii = @(x) exist(x,'file') && strcmp(x(end-5:end),'nii.gz');
+    
+    addParameter(p,'siemens',false,@islogical);
+    addParameter(p,'qmrlab_path',[],@ischar);
+    addParameter(p,'sesFolder',false,@islogical);
+    addParameter(p,'targetDir',[],validDir);
+    
+    parse(p,varargin{:});
+    
+    % Capture session folder flag
+    sesFolder = p.Results.sesFolder; 
+
+    if ismember('ses',keyval)
+        [~,idx]= ismember('ses',keyval);
+        sesVal = keyval{idx+1};
+    else
+       sesVal = [];
+    end
+    
+    if ismember('sub',keyval)
+        [~,idx]= ismember('sub',keyval);
+        subVal = keyval{idx+1};
+    else
+       subVal = SID;
+    end
+    
+    % This env var will be consumed by qMRLab
+    setenv('ISNEXTFLOW','1');
+    setenv('ISBIDS','1');
+
+    if ~isempty(p.Results.qmrlab_path); qMRdir = p.Results.qmrlab_path; end
+
+    try
+        disp('=============================');
+        qMRLabVer;
+    catch
+        warning('Cant find qMRLab. Adding qMRLab_DIR to the path: ');
+        if ~strcmp(qMRdir,'null')
+            qmr_init(qMRdir);
+        else
+            error('Please set qMRLab_DIR parameter in the nextflow.config file.');
+        end
+        qMRLabVer;
+    end
+    
+    data = struct();
+    
+    if ~isempty(p.Results.siemens); issiemens = p.Results.siemens; end
+    
+    data = load_untouch_nii(b1plus_nii);
+    data.img = double(load_nii_data(b1plus_nii));
+
+    % TODO: 
+    % Check if Octave is OK with inputParser (and MATLAB version range)
+    % If so use it to reduce the verbosity below.
+
+    if issiemens
+        data.img = data.img./800;
+    % ISBIDS is set to 1, FitData will expect
+    % inputs to be in relative % (see input_BIDS_units.json)
+    % therefore, we need to multiply it by 100 here
+    data.img = data.img.*100;
+    end
+
+    nii = nii_reset_orient(data.hdr, data.img);
+    data.hdr = nii.hdr;
+    data.img = nii.img;
+
+    
+    % ==== Save Data ====
+    
+    addField = struct();
+
+    addField.BasedOn = {b1plus_nii};
+    if ~isempty(SID)
+        savejson('',addField,[pwd filesep SID '_B1plusmap_unfiltered.json']);
+        save_untouch_nii(data, [pwd filesep SID '_B1plusmap_unfiltered.nii.gz'])
+    else
+        savejson('',addField,[pwd filesep 'B1plusmap_unfiltered.json']);
+        save_untouch_nii(data, [pwd filesep 'B1plusmap_unfiltered.nii.gz'])
+    end
+        
+    if moxunit_util_platform_is_octave
+        warning('on','all');
+    end
+    
+    setenv('ISBIDS','');
+    setenv('ISNEXTFLOW','');
+
+end
+     
+    
+function qmr_init(qmrdir)
+
+run([qmrdir filesep 'startup.m']);
+
+end
\ No newline at end of file