Update PyD to DKE conversion scripts (#210)

* Convert AWF array to float

* Update input file check in dwipy

* Fixed dockerfile bugs (#202)

* Update files to delete

* Update Changelog

* Update PyDesigner version info

* Update des2dke B0 name

* WMTI Calculation Fix (#204)

* Add intra- and extra-axonal diffusivities to WMTI

* Convert `json2fslgrad` from method to func

* Update CHANGELOG

* Update v0.31>>v0.32

* Update doc table of file outputs

* Update README image size

* Change WMTI file names

* Change filenames again

* Minor WMTI bugfixes

* Transpose B0 BVALS in json2fslgrad (#206)

* Update changelog (#207)

* Update PyD to DKE conversion script (#209)

* Rename Extras to extras

* Init FT parameter file

* Allow FWHM res change in DKE param file

* Update PyD to DKE conversion script

* Update changelog

CHANGELOG.rst

@@ -7,7 +7,7 @@ page
 `v0.32`_
 --------
 
-Apr 10, 2020
+Apr 21, 2020
 
 **Added**:
 
@@ -21,6 +21,9 @@ Apr 10, 2020
 * ``json2fslgrad`` now transposes B0s in BVAL file in accordance with
   FSL's gradient scheme
 * Documentation update
+* ``Extras`` directory renamed to ``extras``
+* DKE conversion scripts modified to correctly create ft and dke
+  parameter files
 
 **Removed**:
 

Extras/des2dke.m → extras/des2dke.m

@@ -86,7 +86,7 @@ function des2dke(inDir)
 save(fullfile(p,'gradient_dke.txt'),'Gradient1','-ASCII');
 
 %% Create DKE Parameter File
-fprintf('4: Creating parameter files\n');
+fprintf('4: Creating DKE parameter files\n');
 fid=fopen('dke_parameters.txt'); %Original file
 fout=fullfile(dke_Path,'dke_parameters.txt');% new file
 
@@ -96,9 +96,28 @@ function des2dke(inDir)
     s=fgetl(fid);
     s=strrep(s,'dir-sub-changeme',dke_Path); %s=strrep(s,'A201', subject_list{i}) replace subject
     s=strrep(s,'ndir = changeme',sprintf('ndir = %d',length(b1_idx_new)));
+    s=strrep(s,'bval = changeme',sprintf('bval = [%s]', num2str(unique(bval))));
     s=strrep(s,'fn-gradients-changeme',fullfile(dke_Path,'gradient_dke.txt'));
+    s=strrep(s,'fwhm_img = res-changeme',sprintf('fwhm_img = 0 * [%s]', num2str(hdr.PixelDimensions(1:3),3)));
     fprintf(fidout,'%s\n',s);
 end
 fclose(fid);
 fclose(fidout);
 fprintf('.....Completed.....\n');
+
+%% Create FT Parameter File
+fprintf('4: Creating FT parameter files\n');
+fid=fopen('ft_parameters.txt'); %Original file
+fout=fullfile(dke_Path,'ft_parameters.txt');% new file
+
+fidout=fopen(fout,'w');
+
+while(~feof(fid))
+    s=fgetl(fid);
+    s=strrep(s,'dir-sub-changeme',dke_Path); %s=strrep(s,'A201', subject_list{i}) replace subject
+    fprintf(fidout,'%s\n',s);
+end
+fclose(fid);
+fclose(fidout);
+fprintf('.....Completed.....\n');
+

Extras/dke_parameters.txt → extras/dke_parameters.txt

@@ -15,7 +15,7 @@ preprocess_options.fn_nii = 'dke.nii';       		% four-dimensional nifti image fi
 
 % imaging diffusion weightings and directions
 
-bval = [0 1000 2000];                          		% diffusion weightings (b-values) in s/mm^2 units; the first element of vector must always be 0
+bval = bval-changeme;                          		% diffusion weightings (b-values) in s/mm^2 units; the first element of vector must always be 0
 
 ndir = changeme;                                      	% number of gradient directions; if a scalar value is specified, the number of gradient directions for all b values is set to the scalar; otherwise, a 1-by-(nbval-1) vector should be specified, with each element of the vector corresponding to the number of gradient directions for a nonzero b-value
 
@@ -63,7 +63,7 @@ dti_method.noise_tolerance = 0.09;          		% threshold for outlier detection
 
 % diffusion-weighted image filtering
 
-fwhm_img = 0 * [2.0 2.0 2.0];            		% full width at half maximum (FWHM) (in mm) of Gaussian kernel for smoothing diffusion-weighted images (default: 1.25 * voxel size); a zero value indicates no smoothing
+fwhm_img = res-changeme;            		% full width at half maximum (FWHM) (in mm) of Gaussian kernel for smoothing diffusion-weighted images (default: 1.25 * voxel size); a zero value indicates no smoothing
 
 % Rician noise subtraction
 
@@ -72,7 +72,7 @@ fwhm_noise = 0;                             		% FWHM (in mm) of Gaussian kernel
 
 % parametric map filtering
 
-median_filter_method = 0;                   		% selective median filtering applied to voxels that violate the minimum directional kurtosis constraints (default: 2): (0) no filtering; (1) weak filtering (voxels with less than 15 unviolated constraints will be filtered); (2) strong filtering (voxels with any constraint violation will be filtered)
+median_filter_method = 1;                   		% selective median filtering applied to voxels that violate the minimum directional kurtosis constraints (default: 2): (0) no filtering; (1) weak filtering (voxels with less than 15 unviolated constraints will be filtered); (2) strong filtering (voxels with any constraint violation will be filtered)
 
 % parametric map interpolation
 

extras/ft_parameters.txt

@@ -0,0 +1,40 @@
+%--------------------------------------------------------------------------
+%USER OPTIONS
+%--------------------------------------------------------------------------
+studydir = 'dir-sub-changeme'; %Full path to directory containing DT.mat, KT.mat, and fa.nii files.
+subject_list = {''};         %Specify subject numbers (i.e. {'Subject01','Subject02','Subject03',...}).
+
+%ODF Optimizatinon
+
+    odf_optimization = 1;   %Analyze the kurtosis dODF (1) or skip odf optimization (0). This step must be performed prior to tractography.
+    sd = 4;                 %[3,4, or 5] Sampling distribution to use. See sphericalgrid3(4,5).m documentation for more info.
+    quasiNewton = 1;        %Apply non-linear optimization to increase accuracy of peak detection (1) or use orientations directly from the pre-defined sampling distribution (0).
+    radial_weight = 4;      %Radial weighting power.Recommended radial_weight = 4.  
+    release_memory = 0;     %Do not release memory (0), release memory after each subject (1), or release memory more frequently (2). See User's Guide for additional info.         
+    wrt_flg = 1;            %Write outputs (1) or don't write outputs (0).
+    pre_name = '';          %String to append to the beginning of output names.
+    post_name = '';         %String to append to the end of output names.
+
+%Tractography
+
+    tractography_flg = 1;      %Perform tractography (1) or don't perform tractography (0).
+    fa_threshold = 0.1;        %FA threshold.
+    angle_threshold = 35;      %Angle threshold in degrees.
+    trk_length = 20;           %Minimum tract length in mm.
+    step_size = 1;             %Step size in mm (0 defaults to half of the voxel length).
+    trk_mask = '';             %Path to tracking mask to apply in addition to other tract termination criteria defined above. Should be in the same orientation as the fa.nii image.
+    seed_mask = '';            %Mask within which to put seeds. Should be in the same orientation as the fa.nii image
+    seednum = 1E5;             %Number of random seed points in the tracking mask. 
+    shift = 0.5;               %Shift applied to voxel coordinates in .trk file.
+    output_DTI_trks = 1;       %Include tractography performed from just the diffusion tensor (1) or don't (0).
+    image_orientation = 'LAS'; %Orientation of input image volumes. By convention, spm writes images in 'LAS.'  
+    odf_orientation = 'RAS';   %Orientation of the gradient table used to estimate the diffusion and kurtosis tensors. If SPM is used to estimate the gradient tables, this should be 'LAS.'
+
+
+%Make DSI Studio .fib file
+
+    make_fib_file = 1;      %Make .fib file to read in DSI Studio (1) or skip this step (0).
+    save_odfs = 1;          %Save dODFS in .fib file (1) or not (0). This only affects visualization as orientations are still saved for tractography. 
+    scale_odf = 0.5;        %Affects overall size of odfs in .fib file. This only affects visualization.
+    odf_size = 20000;       %Size of odf_n variables. Reduce this if there are issues with RAM.
+    odf_res = 'low';        %{'low' or 'high'}; Number of points saved in ODFs ~ only affects visualization. Use 'low' to reduce memory requirements and use 'high' for the smoothest dODF surface renderings.