minor updates

func/presurf_MPRAGEise.m

@@ -1,4 +1,4 @@
-function presurf_MPRAGEise(full_path_to_inv2,full_path_to_uni)
+function full_path_to_output = presurf_MPRAGEise(full_path_to_inv2,full_path_to_uni)
 disp(' ');
 disp('+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++');
 disp([datestr(datetime('now')), ' Start MPRAGEising']);
@@ -102,6 +102,8 @@ function presurf_MPRAGEise(full_path_to_inv2,full_path_to_uni)
 uni_nii.fname=fullfile(full_path_to_out,[uni_file_prefix,'_MPRAGEised.nii']);
 spm_write_vol(uni_nii,uni_img_clean);
 
+full_path_to_output = uni_nii.fname;
+
 % Clean Up
 rmdir(fullfile(inv2_file_path,'presurf_biascorrect'),'s');
 %% Fin

presurfer_example.m

@@ -1,10 +1,10 @@
 %% MP2RAGE pre-processing Start-to-finish
-UNI=fullfile(pwd,'sub-42_mp2rage_0p7mm_iso_p3_UNI_Images.nii.gz');
-INV2=fullfile(pwd,'sub-42_mp2rage_0p7mm_iso_p3_INV2.nii.gz');
+UNI=fullfile(pwd,'sub-01_acq-MP2RAGE_mod-UNI_defaced.nii');
+INV2=fullfile(pwd,'sub-01_acq-MP2RAGE_mod-INV2_defaced.nii');
 % ########################################################################
 % STEP - 0 : (optional) MPRAGEise UNI
 % ########################################################################
-presurf_MPRAGEise(INV2,UNI); % Outputs presurf_MPRAGEise directory
+UNI_out = presurf_MPRAGEise(INV2,UNI); % Outputs presurf_MPRAGEise directory
 
 % ########################################################################
 % STEP - 1 : Pre-process INV2 to get STRIPMASK
@@ -15,8 +15,11 @@
 % STEP - 3 : Pre-process UNI to get BRAINMASK
 % ########################################################################
 % Change UNI path to that of the MPRAGEised UNI if Step-0 was done
-UNI = '/path/to/UNI.nii';
-presurf_UNI(UNI); % Outputs presurf_UNI directory
+if exist('UNI_out','var')
+ presurf_UNI(UNI_out); % Outputs presurf_UNI directory
+else
+ presurf_UNI(UNI);
+end
 
 % ########################################################################
 % STEP - 4 : Prepare for Freesurfer