Renaming scripts

Inner modifications to integrate renaming in the implementation, function
names, help section, etc...

Hopefully complete!

hmri_create_B1Map_process.m

@@ -1,10 +1,10 @@
-function [allub1_img] = hmri_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params)
+function [allub1_img] = hmri_create_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params)
 %==========================================================================
 % PURPOSE
 % To mask, pad and smooth the unwrapped B1 map.
 % Part of the hMRI toolbox, B1+ map calculation, EPI SE/STE protocol.
 %
-% FORMAT [allub1_img] = hmri_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params)
+% FORMAT [allub1_img] = hmri_create_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params)
 % INPUT ARGUMENTS (all filenames are 1-element cell arrays)
 % - ub1_img         filename of the unwrapped B1 map  
 % - ustd_img        filename of the unwrapped SD (error) image 

hmri_create_B1Map_unwarp.m

@@ -1,9 +1,9 @@
-function [fmap_img,unwarp_img] = hmri_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params)
+function [fmap_img,unwarp_img] = hmri_create_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params)
 %==========================================================================
 % PURPOSE
 % For B0 undistortion of EPI-based B1 maps, part of the hMRI toolbox.
 %
-% FORMAT [fmap_img,unwarp_img] = hmri_B1Map_unwarp(magfnam, phasefnam, anatfnam, otherfnam, b1map_params)
+% FORMAT [fmap_img,unwarp_img] = hmri_create_B1Map_unwarp(magfnam, phasefnam, anatfnam, otherfnam, b1map_params)
 % INPUT ARGUMENTS
 % - fmfnam          filename of the fieldmap images (must be char) 
 % - anatfnam        filename of the image to be undistorted ("anatomical" reference, i.e. SSQ image)   
@@ -101,7 +101,7 @@
     %----------------------------------------------------------------------
     % Create field map (in Hz) - this routine calls the unwrapping
     %----------------------------------------------------------------------
-    IP.fm = hmri_FieldMap('CreateFieldMap',IP);
+    IP.fm = hmri_create_FieldMap('CreateFieldMap',IP);
 
     % TL: move created maps to outpath
     if IP.maskbrain==1

hmri_create_FieldMap.m

@@ -1,4 +1,4 @@
-function varargout = hmri_FieldMap(varargin)
+function varargout = hmri_create_FieldMap(varargin)
 % This is a fraction of the FieldMap script (case 'createfieldmap')
 % rewritten for the hMRI toolbox in order to make use of the original
 % SPM12's FieldMap script wherever no modification is required. The
@@ -8,13 +8,13 @@
 % Implementation following FieldMap version:
 % $Id: FieldMap.m 6994 2017-01-26 16:19:14Z guillaume $
 % 
-% FORMAT IP.fm = hmri_FieldMap('CreateFieldMap',IP);
+% FORMAT IP.fm = hmri_create_FieldMap('CreateFieldMap',IP);
 %=======================================================================
 
 persistent IP            % Input and results
 
 if nargin == 0
-   warning('Can only be called for map creation.\nFORMAT: FM = hmri_FieldMap(''CreateFieldMap'',IP);');
+   warning('Can only be called for map creation.\nFORMAT: FM = hmri_create_FieldMap(''CreateFieldMap'',IP);');
    return;
 else
    Action = varargin{1};
@@ -63,7 +63,7 @@
          if IP.maskbrain==1 
             IP.fmagP = FieldMap('Magnitude',IP);
             % IP.uflags.bmask = pm_brain_mask(IP.fmagP,IP.mflags);
-            IP.uflags.bmask = hmri_pm_brain_mask(IP.fmagP,IP.mflags);
+            IP.uflags.bmask = hmri_create_pm_brain_mask(IP.fmagP,IP.mflags);
             varargout{2} = IP.fmagP;
          end
 

hmri_create_MTProt.m

@@ -1,4 +1,4 @@
-function [fR1, fR2s, fMT, fA, PPDw, PT1w]  = hmri_MTProt(jobsubj, P_trans, P_receiv) %#ok<*STOUT>
+function [fR1, fR2s, fMT, fA, PPDw, PT1w]  = hmri_create_MTProt(jobsubj, P_trans, P_receiv) %#ok<*STOUT>
 
 % Evaluation function for multi-contrast multi-echo FLASH protocol
 % P_mtw, P_pdw, P_t1w (retrieved from jobsubj.raw_mpm): MTw, PDw, T1w
@@ -578,7 +578,7 @@
 
     % Use masked MT image to calculate transformation for ACPC realignment
     % (to increase robustness in segmentation):
-    [~,R] = hmri_comm_adjust(1,V_MT.fname,V_MT.fname,8,0,fullfile(spm('Dir'),'canonical','avg152T1.nii')); 
+    [~,R] = hmri_create_comm_adjust(1,V_MT.fname,V_MT.fname,8,0,fullfile(spm('Dir'),'canonical','avg152T1.nii')); 
 
     % Collect all images from all defined output directories:
     allpaths = jobsubj.path;

hmri_create_RFsens.m

@@ -1,4 +1,4 @@
-function jobsubj = hmri_RFsens(jobsubj)
+function jobsubj = hmri_create_RFsens(jobsubj)
 % RF sensitivity calculation as part of the hmri toolbox
 % Based on a script by Daniel Papp
 % Wellcome Trust Centre for Neuroimaging (WTCN), London, UK.

hmri_create_b1map.m

@@ -1,7 +1,7 @@
-function P_trans = hmri_run_b1map(jobsubj)
+function P_trans = hmri_create_b1map(jobsubj)
 
 %% Processing of B1 maps for B1 bias correction
-% FORMAT P_trans = hmri_run_b1map(jobsubj)
+% FORMAT P_trans = hmri_create_b1map(jobsubj)
 %    jobsubj - are parameters for one subject out of the job list.
 %    NB: ONE SINGLE DATA SET FROM ONE SINGLE SUBJECT IS PROCESSED HERE,
 %    LOOP OVER SUBJECTS DONE AT HIGHER LEVEL.
@@ -164,13 +164,15 @@
 % Corresponding scanning protocol/sequence: al_B1mapping
 % Input: 11 pairs of (SE, STE) images for B1 map calculation and 3 images
 % for B0 map calculation.
-% This macro calls the functions hmri_B1Map_unwarp and hmri_B1Map_process
-% for correction of image distortions, padding and smoothing of the images.
+% This macro calls the functions hmri_create_B1Map_unwarp and
+% hmri_create_B1Map_process for correction of image distortions, padding
+% and smoothing of the images. 
 % Output:
 %     - distorted B1 (B1map_*) and error (SDmap_*) maps
 %     - undistorted B1 (uB1map_*) and error (uSDmap_*) maps
 %     - undistorted, masked and padded B1 maps (muB1map_*)
-%     - undistorted, masked, padded and smoothed B1 maps (smuB1map_*) i.e. FULLY PROCESSED
+%     - undistorted, masked, padded and smoothed B1 maps (smuB1map_*)
+%                                                   i.e. FULLY PROCESSED
 % At each voxel, this macro selects the 5 pairs of (SE,STE image) (out of
 % 11) with maximum signal amplitude in the SE images.
 % The sum of square image of all SE images is created (SumOfSq) and
@@ -295,7 +297,7 @@
 otherfnam{2} = W_save.fname;
 
 % unwarp
-[fmap_img,unwarp_img] = hmri_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params);
+[fmap_img,unwarp_img] = hmri_create_B1Map_unwarp(fmfnam, anatfnam, otherfnam, b1map_params);
 uanat_img{1} = unwarp_img{1}.fname;
 ub1_img{1} = unwarp_img{2}.fname;
 ustd_img{1} = unwarp_img{3}.fname;
@@ -341,7 +343,7 @@
 %--------------------------------------------------------------------------
 fpm_img{1} = fmap_img{1};
 vdm_img{1} = fmap_img{2};
-[allub1_img] = hmri_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params);
+[allub1_img] = hmri_create_B1Map_process(ub1_img,ustd_img,vdm_img,fpm_img,b1map_params);
 
 % set metadata for processing B1 images
 % define generic header for B1 process

hmri_create_comm_adjust.m

@@ -1,4 +1,4 @@
-function [M,R] = hmri_comm_adjust(option,Ref,Other,Nits,doshear,Template)
+function [M,R] = hmri_create_comm_adjust(option,Ref,Other,Nits,doshear,Template)
 
 % This function is a version of comm_adjust.m customized for T1 like
 % images, i.e. MT images. Now it is necessary to define as input parameter

hmri_create_pm_brain_mask.m

@@ -1,10 +1,10 @@
-function bmask = hmri_pm_brain_mask(P,flags)
+function bmask = hmri_create_pm_brain_mask(P,flags)
 % Calculate a brain mask in hMRI Toolbox
 % This is pm_brain_mask (SPM12/toolbox/FieldMap) modified for the hMRI
-% toolbox. Calls hmri_pm_segment instead of pm_segment. This is the only
-% modification, syntax is unchanged otherwise.
+% toolbox. Calls hmri_create_pm_segment instead of pm_segment. This is the
+% only modification, syntax is unchanged otherwise.
 %
-% FORMAT bmask = hmri_pm_brain_mask(P,flags)
+% FORMAT bmask = hmri_create_pm_brain_mask(P,flags)
 %
 % P - is a single pointer to a single image
 %
@@ -50,8 +50,8 @@
 % seg_flags.estimate.reg=flags.reg;
 % seg_flags.graphics = flags.graphics;
 % VO=pm_segment(P.fname,flags.template,seg_flags);
-% % In hmri_pm_brain_mask, replaced by:
-VO = hmri_pm_segment(P.fname);
+% % In hmri_create_pm_brain_mask, replaced by:
+VO = hmri_create_pm_segment(P.fname);
 
 bmask=double(VO(1).dat)+double(VO(2).dat)+double(VO(3).dat)>0;
 

hmri_create_pm_segment.m

@@ -1,9 +1,9 @@
-function VO = hmri_pm_segment(InputImage)
+function VO = hmri_create_pm_segment(InputImage)
 % To segment the brain and extract a brain mask in the hMRI Toolbox
 % This function replaces pm_segment used in the FieldMap toolbox
-% (SPM12/toolbox/FieldMap). Used in hmri_pm_brain_mask.
+% (SPM12/toolbox/FieldMap). Used in hmri_create_pm_brain_mask.
 %
-% FORMAT: VO = hmri_pm_segment(P.fname).
+% FORMAT: VO = hmri_create_pm_segment(P.fname).
 %
 %========================================================================== 
 % Written by Lester Melie-Garcia

hmri_create_process_data_spec.m

@@ -1,4 +1,4 @@
-function job = hmri_process_data_spec(job)
+function job = hmri_create_process_data_spec(job)
 if isfield(job.data_spec, 'sdata_multi')
     % ---- MT ----
     s = 1;

hmri_create_unicort.m

@@ -1,5 +1,5 @@
-function out = hmri_run_unicort(P_PDw, P_R1, jobsubj)
-% function P = hmri_run_unicort(P_PDw, P_R1, jobsubj)
+function out = hmri_create_unicort(P_PDw, P_R1, jobsubj)
+% function P = hmri_create_unicort(P_PDw, P_R1, jobsubj)
 % P_PDw: proton density weighted FLASH image (small flip angle image) for
 % masking
 % P_R1: R1 (=1/T1) map estimated from dual flip angle FLASH experiment

hmri_proc_MPMsmooth.m

@@ -1,9 +1,9 @@
-function fn_out = hmri_MPMsmooth(fn_wMPM, fn_mwTC, fn_TPM, fwhm, l_TC)
+function fn_out = hmri_proc_MPMsmooth(fn_wMPM, fn_mwTC, fn_TPM, fwhm, l_TC)
 % Applying tissue specific smoothing, aka. weighted averaging, in order to 
 % limit partial volume effect. 
 % 
 % FORMAT
-%   fn_out = hmri_MPMsmooth(fn_wMPM, fn_mwTC, fn_TPM, fwhm)
+%   fn_out = hmri_proc_MPMsmooth(fn_wMPM, fn_mwTC, fn_TPM, fwhm)
 % 
 % INPUT
 % - fn_wMPM : filenames (char array) of the warped MPM, i.e. the

hmri_run_create.m

@@ -1,11 +1,11 @@
-function out = hmri_run_mpr(job)
+function out = hmri_run_create(job)
 %==========================================================================
 % PURPOSE
 % Calculation of multiparameter maps using B1 maps for B1 bias correction.
 % If no B1 maps available, one can choose not to correct for B1 bias or
 % apply UNICORT.
 %==========================================================================
-job = hmri_process_data_spec(job);
+job = hmri_create_process_data_spec(job);
 
 out.R1 = {};
 out.R2s = {};
@@ -17,7 +17,7 @@
 % each subject:
 for in=1:numel(job.subj)
     local_job.subj = job.subj(in);
-    out_temp       = hmri_mpr_local(local_job);
+    out_temp       = hmri_create_local(local_job);
     out.subj(in)   = out_temp.subj(1);
     out.R1{end+1}  = out.subj(in).R1{1};
     out.R2s{end+1} = out.subj(in).R2s{1};
@@ -30,7 +30,7 @@
 %% =======================================================================%
 % LOCAL SUBFUNCTION (PROCESSING FOR ONE SUBJET)
 %=========================================================================%
-function out_loc = hmri_mpr_local(job)
+function out_loc = hmri_create_local(job)
 
 % determine output directory path
 try 
@@ -61,22 +61,22 @@
 job.subj.path.respath = respath;
 
 % run B1 map calculation for B1 bias correction
-P_trans = hmri_run_b1map(job.subj);
+P_trans = hmri_create_b1map(job.subj);
 
 % check, if RF sensitivity profile was acquired and do the recalculation
 % accordingly
 if ~isfield(job.subj.sensitivity,'RF_none')
-  job.subj = hmri_RFsens(job.subj);
+  job.subj = hmri_create_RFsens(job.subj);
 end
 
 P_receiv = [];
 
-% run hmri_MTProt to evaluate the parameter maps
-[fR1, fR2s, fMT, fA, PPDw, PT1w]  = hmri_MTProt(job.subj, P_trans, P_receiv);
+% run hmri_create_MTProt to evaluate the parameter maps
+[fR1, fR2s, fMT, fA, PPDw, PT1w]  = hmri_create_MTProt(job.subj, P_trans, P_receiv);
 
 % apply UNICORT if required, and collect outputs:
 if strcmp(job.subj.b1_type,'UNICORT')
-    out_unicort = hmri_run_unicort(PPDw, fR1, job.subj);
+    out_unicort = hmri_create_unicort(PPDw, fR1, job.subj);
     out_loc.subj.R1  = {out_unicort.R1u};
 else
     out_loc.subj.R1  = {fR1};

hmri_run_proc_smooth.m

@@ -47,7 +47,7 @@
         fn_mwTC{jj} = job.vols_tc{jj}{i_subj};
     end
 
-    fn_out = hmri_MPMsmooth(char(fn_wMPM), char(fn_mwTC), fn_TPM, job.fwhm, l_TC);
+    fn_out = hmri_proc_MPMsmooth(char(fn_wMPM), char(fn_mwTC), fn_TPM, job.fwhm, l_TC);
 
     for jj = 1:n_TCs
         for kk = 1:n_pams

tbx_cfg_hmri.m

@@ -31,6 +31,6 @@
     'and will include a number of (as yet unspecified) extensions in ',...
     'future updates.  Please report any bugs or problems to [email protected].']
     }';
-hmri.values  = {tbx_scfg_hmri_crm tbx_scfg_hmri_proc };
+hmri.values  = {tbx_scfg_hmri_create tbx_scfg_hmri_proc };
 end
 

tbx_scfg_hmri_create.m

@@ -1,4 +1,4 @@
-function crm = tbx_scfg_hmri_crm
+function crm = tbx_scfg_hmri_create
 % Configuration file for the "histological MRI" (hMRI) toolbox
 % Previously named "Voxel-Based Quantification" (VBQ)
 % -> Dealing with the creation of the maps
@@ -291,8 +291,8 @@
 data_spec.val    = { sdata };
 create_mpr.val     = { data_spec };
 create_mpr.help    = {'hMRI map creation can handle data sets with and without B0/B1 maps.'};
-create_mpr.prog    = @hmri_run_mpr;
-create_mpr.vout    = @vout_create_mpr;
+create_mpr.prog    = @hmri_run_create;
+create_mpr.vout    = @vout_create;
 % ---------------------------------------------------------------------
 % crm Create maps
 % ---------------------------------------------------------------------
@@ -309,13 +309,12 @@
 % ========================================================================
 %% VOUT & OTHER SUBFUNCTIONS
 % ========================================================================
-% The RUN functions :
-% - out = hmri_run_mpr_b0_b1(job)
-% - out = hmri_run_mpr_unicort(job)
-% are defined separately.
+% The RUN function:
+% - out = hmri_run_create(job)
+% is defined separately.
 %_______________________________________________________________________
 
-function dep = vout_create_mpr(job)
+function dep = vout_create(job)
 % This depends on job contents, which may not be present when virtual
 % outputs are calculated.