Fix 'prefs.rest'.

Use 'prefs.rest' instead of 'prefs.rest_default'.

common/ea_prefs_default.m

@@ -49,8 +49,8 @@
 prefs.tonemap='heuristic'; % set to 'albada' to change to datadriven mode
 
 %% connectome files:
-prefs.rest_prefix='res*.nii'; % raw resting state fMRI data search string
-prefs.rest_default='rest.nii'; % default for dcm2nii export.
+prefs.rest_searchstring='rest*.nii'; % raw resting state fMRI data search string
+prefs.rest='rest.nii'; % default for dcm2nii export.
 
 %% connectome settings:
 prefs.lc.struc.maxdist=2; % maximal distance to form a connection (between fiber terminals and voxel centers, in mm).
@@ -106,7 +106,7 @@
 prefs.mrcoreg.writeoutcoreg=0; % set default to 0 to prevent writing out coregistration transformation
 
 %% Subcortical refine (Post to Pre):
-prefs.scrf.tonemap='tp_'; % can set to '' if want to use non-tonemapped CTs for brainshift correction (default = 'tp_'). 
+prefs.scrf.tonemap='tp_'; % can set to '' if want to use non-tonemapped CTs for brainshift correction (default = 'tp_').
 
 %% Atlas-Sets:
 prefs.atlases.default='DISTAL Minimal (Ewert 2017)';

connectomics/ea_genmodlist.m

@@ -48,15 +48,15 @@
         sf(cnt)=2;
         cnt=cnt+1;
     end
-    
+
     % fMRI - raw files:
-    ffis=dir([directory,'res*.nii']);
+    ffis=dir([directory, options.prefs.rest_searchstring]);
     for ff=1:length(ffis);
         [~,modlist{cnt}]=fileparts(ffis(ff).name);
         sf(cnt)=2;
         cnt=cnt+1;
     end
-    
+
 end
 
 % check for already processed maps in case of predict module
@@ -82,7 +82,7 @@
 
 
 if vat
-   resdir=dir([directory,options.prefs.rest_prefix]);
+   resdir=dir([directory,options.prefs.rest_searchstring]);
 
    for rd=1:length(resdir)
        [~,fn,ext]=fileparts(resdir(rd).name);

connectomics/ea_perform_lc.m

@@ -47,7 +47,7 @@ function ea_perform_lc(options)
     disp(['*** Performing functional parts of LEAD-Connectome...']);
 
     % get files with rs-fMRI data
-    restfiles = dir([options.root,options.patientname,filesep,options.prefs.rest_prefix]);
+    restfiles = dir([options.root,options.patientname,filesep,options.prefs.rest_searchstring]);
 
     % get number of files with rs-fMRI data
     options.prefs.n_rest = numel(restfiles);

ea_imageclassifier.m

@@ -318,7 +318,7 @@ function ea_keystr(icfig,event,handles)
         tmpoutdir=getappdata(handles.imclassf,'tmpoutdir');
         [~,pt]=fileparts(tmpoutdir);
         prefs=ea_prefs(pt);
-        finishandclose(handles,prefs.rest_default);
+        finishandclose(handles,prefs.rest);
     case '1'
         finishandclose(handles,'anat_t1.nii');
     case '2'
@@ -399,7 +399,7 @@ function restpush_Callback(hObject, eventdata, handles)
 
 [~,pt]=fileparts(tmpoutdir);
 prefs=ea_prefs(pt);
-finishandclose(handles,prefs.rest_default);
+finishandclose(handles,prefs.rest);
 
 
 % --- Executes on button press in dtipush.

helpers/ea_getbasefilenames.m

@@ -21,7 +21,7 @@
     prefs.sagnii_unnormalized
     prefs.rawctnii_unnormalized
     prefs.ctnii_coregistered
-    prefs.rest_default
+    prefs.rest
     prefs.dti
 };
 

helpers/ea_mnifigure.m

@@ -186,8 +186,8 @@
 options.prefs.gsagnii = 'glpostop_sag.nii';
 options.prefs.gctnii = 'glpostop_ct.nii';
 options.prefs.tp_gctnii = 'tp_glpostop_ct.nii';
-options.prefs.rest_prefix = 'res*.nii';
-options.prefs.rest_default = 'rest.nii';
+options.prefs.rest_searchstring = 'rest*.nii';
+options.prefs.rest = 'rest.nii';
 options.prefs.lc.struc.maxdist = 2;
 options.prefs.lc.struc.minlen = 3;
 options.prefs.lc.graphsurfc = [0.2081 0.1663 0.5292];
@@ -268,7 +268,6 @@
 options.prefs.prenii_pd = 'lanat_pd.nii';
 options.prefs.gprenii_t1 = 'glanat_t1.nii';
 options.prefs.gprenii_pd = 'glanat_pd.nii';
-options.prefs.rest = 'rest.nii';
 options.prefs.vat.gm = 'atlas';
 options.prefs.firstrun = 'off';
 options.prefs.machine.d2.col_overlay = 0;