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fahsuanlin · Mar 10, 2024 · 3c33d03 · 3c33d03
1 parent 4bd8c93
commit 3c33d03
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diff --git a/scripts/bb_register_blipdown_init.dat b/scripts/bb_register_blipdown_init.dat
@@ -0,0 +1,9 @@
+011624
+5
+5
+0.250000
+   0.1286    0.9913    0.0271   10.7043
+   -0.0360   -0.0226    0.9991  -10.4805
+    0.9910   -0.1296    0.0329   -0.7073
+         0         0         0    1.0000
+round
diff --git a/scripts/bb_register_blipup_init.dat b/scripts/bb_register_blipup_init.dat
@@ -0,0 +1,9 @@
+011624
+5
+5
+0.250000
+   -0.0308   -0.9992    0.0248   -0.8783
+   -0.0322    0.0259    0.9991  -10.8010
+    0.9990   -0.0301    0.0331    1.5833
+         0         0         0    1.0000
+round
diff --git a/scripts/register_init_epi_blipdown.m b/scripts/register_init_epi_blipdown.m
@@ -0,0 +1,40 @@
+close all; clear all;
+
+subject='011624';
+hemi='rh';
+surf='white';
+
+
+file_overlay_register='./bb_register_blipdown_init.dat';
+%file_overlay_vol='epi__epi_blipdown.mgh';
+file_overlay_vol='epi__epi_blipdown_fliplr.mgh'; %use this one because SMS-InI has flipped A-P direction compared to EPI.
+overlay_threshold=[];
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+setenv('SUBJECTS_DIR','/Users/fhlin/workspace/smsini_blipud/subjects/'); %for MAC/Linux
+%setenv('SUBJECTS_DIR','D:\fhlin\Users\fhlin\workspace\seeg\subjects'); %for PC
+
+mri=MRIread(sprintf('/Users/fhlin/workspace/smsini_blipud/subjects/%s/mri/orig.mgz',subject)); %for MAC/Linux
+%mri=etc_MRIread('D:\fhlin\Users\fhlin\workspace\seeg\subjects\2036\mri\orig.mgz'); %for PC
+
+%load the Talairach transformation matrix from the "pre-OP" data
+talxfm=etc_read_xfm('file_xfm',sprintf('%s/%s/mri/transforms/talairach.xfm',getenv('SUBJECTS_DIR'),subject)); %for MAC/Linux
+%talxfm=etc_read_xfm('file_xfm','D:\fhlin\Users\fhlin\workspace\seeg\subjects\2036\mri\transforms\talairach.xfm'); %for PC
+
+%%% volume overlay
+f=MRIread(file_overlay_vol);
+
+r=etc_read_xfm('file_xfm',file_overlay_register);
+
+%prepare overlay volume matched to the underlay volume
+vol = etc_MRIvol2vol(f,mri,r,'frames',[1]); %only the first volume
+
+%prepare overlay surface
+vol2surf = etc_MRIvol2surf(f,surf,r,'subject',subject,'frames',[1],'hemi',hemi);
+
+%etc_render_fsbrain('surf',surf,'hemi',hemi,'subject',subject,'vol',mri,'talxfm',(talxfm),'overlay_vol',vol,'overlay_value',vol2surf,'overlay_vertex',[1:size(vol2surf,1)]-1,'overlay_threshold',overlay_threshold,'overlay_flag_paint_on_cortex',0);
+etc_render_fsbrain('surf',surf,'hemi',hemi,'subject',subject,'vol',mri,'talxfm',(talxfm),'overlay_vol',vol,'overlay_threshold',overlay_threshold,'overlay_flag_paint_on_cortex',0);
+
+%1. calcualte r * overlay_xfm after exporting the registration in Matlab work space
+%
+%2. check initial registration at command line: tkregisterfv --mov smsini_mb_run_1_ref.mgh --reg bb_register_init.dat --surfs  --sd /Users/fhlin/workspace/smsini_blipud/subjects/
diff --git a/scripts/register_init_epi_blipup.m b/scripts/register_init_epi_blipup.m
@@ -0,0 +1,39 @@
+close all; clear all;
+
+subject='011624';
+hemi='rh';
+surf='white';
+
+
+file_overlay_register='./bb_register_blipup_init.dat';
+file_overlay_vol='epi__epi_blipup.mgh';
+overlay_threshold=[];
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+setenv('SUBJECTS_DIR','/Users/fhlin/workspace/smsini_blipud/subjects/'); %for MAC/Linux
+%setenv('SUBJECTS_DIR','D:\fhlin\Users\fhlin\workspace\seeg\subjects'); %for PC
+
+mri=MRIread(sprintf('/Users/fhlin/workspace/smsini_blipud/subjects/%s/mri/orig.mgz',subject)); %for MAC/Linux
+%mri=etc_MRIread('D:\fhlin\Users\fhlin\workspace\seeg\subjects\2036\mri\orig.mgz'); %for PC
+
+%load the Talairach transformation matrix from the "pre-OP" data
+talxfm=etc_read_xfm('file_xfm',sprintf('%s/%s/mri/transforms/talairach.xfm',getenv('SUBJECTS_DIR'),subject)); %for MAC/Linux
+%talxfm=etc_read_xfm('file_xfm','D:\fhlin\Users\fhlin\workspace\seeg\subjects\2036\mri\transforms\talairach.xfm'); %for PC
+
+%%% volume overlay
+f=MRIread(file_overlay_vol);
+
+r=etc_read_xfm('file_xfm',file_overlay_register);
+
+%prepare overlay volume matched to the underlay volume
+vol = etc_MRIvol2vol(f,mri,r,'frames',[1]); %only the first volume
+
+%prepare overlay surface
+vol2surf = etc_MRIvol2surf(f,surf,r,'subject',subject,'frames',[1],'hemi',hemi);
+
+%etc_render_fsbrain('surf',surf,'hemi',hemi,'subject',subject,'vol',mri,'talxfm',(talxfm),'overlay_vol',vol,'overlay_value',vol2surf,'overlay_vertex',[1:size(vol2surf,1)]-1,'overlay_threshold',overlay_threshold,'overlay_flag_paint_on_cortex',0);
+etc_render_fsbrain('surf',surf,'hemi',hemi,'subject',subject,'vol',mri,'talxfm',(talxfm),'overlay_vol',vol,'overlay_threshold',overlay_threshold,'overlay_flag_paint_on_cortex',0);
+
+%1. calcualte r * overlay_xfm after exporting the registration in Matlab work space
+%
+%2. check initial registration at command line: tkregisterfv --mov smsini_mb_run_1_ref.mgh --reg bb_register_init.dat --surfs  --sd /Users/fhlin/workspace/smsini_blipud/subjects/
diff --git a/scripts/smsini_tsnr.m b/scripts/smsini_tsnr.m
@@ -0,0 +1,65 @@
+close all; clear all;
+
+stc_file_stem={
+    'smsini_mb_run_1_acc';
+    'smsini_mb_run_2_acc';
+    };
+
+for file_idx=1:length(stc_file_stem)
+    for hemi=1:2
+        switch hemi
+            case 1
+                hemi_str='lh';
+            case 2
+                hemi_str='rh';
+        end;
+
+        fn=sprintf('%s-%s.stc',stc_file_stem{file_idx},hemi_str);
+        [stc,v{hemi}]=inverse_read_stc(fn);
+
+
+        [tsnr{file_idx,hemi}]=etc_tsnr('stc',stc,'exclude_time',[1:10]);
+
+        fn_out=sprintf('%s_tsnr-%s.stc',stc_file_stem{file_idx},hemi_str);
+
+        inverse_write_stc(repmat(tsnr{file_idx,hemi}(:),[1 5]),v{hemi},0,100,fn_out);
+    end;
+
+    for hemi=1:2
+        switch hemi
+            case 1
+                hemi_str='lh';
+            case 2
+                hemi_str='rh';
+        end;
+
+        etc_render_fsbrain('subject','011624','overlay_vertex',v{hemi},'overlay_value',tsnr{file_idx,hemi}(:),'overlay_threshold',[50 500]);
+
+
+        %generate image outputs
+        for view_idx=1:2
+            switch(hemi_str)
+                case 'lh'
+                    if(view_idx==1)
+                        view(90,0);
+                        view_str='med';
+                    elseif(view_idx==2)
+                        view(-90,0);
+                        view_str='lat';
+                    end;
+                case 'rh'
+                    if(view_idx==1)
+                        view(-90,0);
+                        view_str='med';
+                    elseif(view_idx==2)
+                        view(90,0);
+                        view_str='lat';
+                    end;
+            end;
+            hgexport(gcf,sprintf('%s_%s_%s.png',stc_file_stem{file_idx},hemi_str,view_str), hgexport('factorystyle'),'Format','png');
+        end;
+        close;
+    end;
+end;
+
+save smsini_tsnr.mat tsnr;