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Author: weikanggong

Diff for: Script_to_Run.m

@@ -27,12 +27,16 @@
 %Please set the following parameters for rest fMRI data preprocessing
 
 % Data Directory (Be sure your data structure is correct!!)
-workingDir='/home/wkgong/MATLAB/mycode/Rest_Preprcessing/example';
+workingDir='/home/gongweikang/Depression/xinan';
 
-% Slice Timing TR (in second)
-TR=2.5;
 
-% Slice order (1: bottom up, 2: top down, 3: interleaved+bottem up, 4: interleaved+top down)
+% whether do slicetiming
+Is_slicetiming=1;
+
+% Slice Timing TR (in second) (useful for filter)
+TR=2;
+
+% Slice order (1: bottom up, 2: top down, 3: interleaved+bottem up, 4: interleaved+top down, 'file.txt': specify slice direction)
 slice_order=3;
 
 % Spatial Gaussian Kernel Full-Width at Half Maximum (in mm)
@@ -44,29 +48,32 @@
 % bandpass ([low,high] in Hz)
 bandpass=[0.01,0.1];
 
+
+% The standard space to which each image is mapped.
+resolution='3mm';
+
 % Maximum Memory allowed for Wavelet Despiking (in GB)
 memory=3;
 
 % Number of processors 
-n_core=20;
+n_core=19;
 
 %Be sure that memory*n_core < maximum memory allowed!!
 
 
 
 %% Main Function
+options.Is_slicetiming=Is_slicetiming;
 options.TR=TR;
 options.slice_order=slice_order;
 options.FWHM=FWHM;
 options.motion=motion;
 options.memory=memory;
 options.n_core=n_core;
 options.bandpass=bandpass;
-
+options.resolution=resolution;
 g_MainFunction(workingDir,options);
 
 
 
 
-
-

Diff for: g_Func2std_mapping.m

@@ -1,31 +1,32 @@
 
-function g_Func2std_mapping(infile1,infile2)
+function g_Func2std_mapping(infile1,infile2,resolution)
 
 disp('Mapping FunImg to Standard Space...')
 
+%resolution='3mm';
 
 d1=which('g_Func2std_mapping');
 d1=strrep(d1,'g_Func2std_mapping.m','');
-reff1=[d1,'MNI152_T1_3mm_brain'];
+reff1=[d1,'MNI152_T1_',resolution,'_brain'];
 folder='7_FunImg_to_Std';
 mkdir(folder);
 unix(['mv Func2std.nii.gz ',folder]);
 unix(['mv std2Func.nii.gz ',folder]);
 unix(['mv Fun2strBBR ',folder]);
 
-command=['applywarp --ref=',reff1,' --in=',infile1,' --warp=./7_FunImg_to_Std/Func2std --rel --out=FunImg_3mmStdSpace --interp=sinc'];
+command=['applywarp --ref=',reff1,' --in=',infile1,' --warp=./7_FunImg_to_Std/Func2std --rel --out=FunImg_',resolution,'StdSpace --interp=sinc'];
 unix(command);
 
-command=['applywarp --ref=',reff1,' --in=',infile2,' --warp=./7_FunImg_to_Std/Func2std --rel --out=FunImg_3mmStdSpace_NoGlobalSignal --interp=sinc'];
+command=['applywarp --ref=',reff1,' --in=',infile2,' --warp=./7_FunImg_to_Std/Func2std --rel --out=FunImg_',resolution,'StdSpace_NoGlobalSignal --interp=sinc'];
 unix(command);
 
 
 
-movefile('FunImg_3mmStdSpace.nii.gz',folder);
-movefile('FunImg_3mmStdSpace_NoGlobalSignal.nii.gz',folder);
+movefile(['FunImg_',resolution,'StdSpace.nii.gz'],folder);
+movefile(['FunImg_',resolution,'StdSpace_NoGlobalSignal.nii.gz'],folder);
 
 disp('Finished!');
 
 
 
-end
+end

Diff for: g_MainFunction.m

@@ -42,7 +42,7 @@ function g_MainFunction(workingDir,options)
             outfile='Slice_Timing_Corrected';
         else
             infile=['./',folder,'/',outfile];
-            [outfile,folder]=g_slicetiming(infile,options.TR,options.slice_order);
+            [outfile,folder]=g_slicetiming(infile,options.Is_slicetiming,options.TR,options.slice_order);
         end
 
 
@@ -122,15 +122,15 @@ function g_MainFunction(workingDir,options)
         end
 
         %fun2str2std
-        f9=dir('./7_FunImg_to_Std/FunImg_4mmStdSpace.nii.gz');
+        f9=dir(['./7_FunImg_to_Std/FunImg_',options.resolution,'StdSpace.nii.gz']);
         if length(f9)==1
             disp('FunImg has been normalized, omit this step...');
             unix('rm Func2std.nii.gz');
             unix('rm std2Func.nii.gz');
         else
             infile1=['./',folder,'/',outfile1];
             infile2=['./',folder,'/',outfile2];
-            g_Func2std_mapping(infile1,infile2)
+            g_Func2std_mapping(infile1,infile2,options.resolution)
         end
 
         %plot picture

Diff for: g_T1preprocessing.m

@@ -22,7 +22,7 @@
     disp('Done...');
     %bet
     disp('Brain extraction...');
-    command3=['bet cc_',f1,' bet_cc_',f1,' -m'];
+    command3=['bet cc_',f1,' bet_cc_',f1,' -m -f 0.3'];
     unix(command3);
     disp('Done...');
 

Diff for: g_regressWmCsf_and_filter.m

@@ -80,9 +80,9 @@
 
 if TR~=0
     %regress them out and do temporal filtering
-    command10=['3dTproject -ort csf_wm_motion.1D -prefix regressed_and_filtered.nii.gz -passband ',num2str(bandpass(1)),' ',num2str(bandpass(2)),' -input ',infile,'.nii.gz -dt ',TR];
+    command10=['3dTproject -ort csf_wm_motion.1D -prefix regressed_and_filtered.nii.gz -passband ',num2str(bandpass(1)),' ',num2str(bandpass(2)),' -input ',infile,'.nii.gz -dt ',num2str(TR)];
     unix(command10);
-    command10=['3dTproject -ort csf_wm_motion_global.1D -prefix regressed_and_filtered_NoGlobalSignal.nii.gz -passband ',num2str(bandpass(1)),' ',num2str(bandpass(2)),' -input ',infile,'.nii.gz -dt ',TR];
+    command10=['3dTproject -ort csf_wm_motion_global.1D -prefix regressed_and_filtered_NoGlobalSignal.nii.gz -passband ',num2str(bandpass(1)),' ',num2str(bandpass(2)),' -input ',infile,'.nii.gz -dt ',num2str(TR)];
     unix(command10);
 else
     command10=['3dTproject -ort csf_wm_motion.1D -prefix regressed_and_filtered.nii.gz -passband ',num2str(bandpass(1)),' ',num2str(bandpass(2)),' -input ',infile,'.nii.gz'];

Diff for: g_slicetiming.m

@@ -1,11 +1,11 @@
-function [outfile,folder]=g_slicetiming(infile,TR,slice_order)
+function [outfile,folder]=g_slicetiming(infile,Is_slicetiming,TR,slice_order)
 
 
 
 %slice timing
 disp('Slice timing correction...');
 
-if TR==0
+if Is_slicetiming==0
     disp(['TR is ',num2str(TR),'...']);   
     outfile='Slice_Timing_Corrected';
     folder='2_Slice_Timing_Corrected';
@@ -29,24 +29,22 @@
         disp('Slice order is bottom-up..')
         command=['slicetimer -i ',infile,' -o ',outfile,' -r ',TR];
         unix(command);
-    end
-    
-    if slice_order==2
+    elseif slice_order==2
         disp('Slice order is top-down..')
         command=['slicetimer -i ',infile,' -o ',outfile,' --down -r ',TR];
         unix(command);
-    end
-    
-    if slice_order==3
+    elseif slice_order==3
         disp('Slice order is interleaved and bottom up..')
         command=['slicetimer -i ',infile,' -o ',outfile,' --odd -r ',TR];
         unix(command);
-    end
-    
-    if slice_order==4
+    elseif slice_order==4
         disp('Slice order is interleaved and top down..')
         command=['slicetimer -i ',infile,' -o ',outfile,' --odd --down -r ',TR];
         unix(command);
+    else
+        disp('Slice order is specified elsewhere..')
+        command=['slicetimer -i ',infile,' -o ',outfile,' -r ',TR,' --ocustom=',slice_order];
+        unix(command);
     end
 
     movefile([outfile,'.nii.gz'],folder);