diff --git a/pRF/README.txt b/pRF/README.txt index 65b2d4c..cc6fd80 100644 --- a/pRF/README.txt +++ b/pRF/README.txt @@ -1,8 +1,8 @@ ****************************** README on pRF -Created : "Feb 27 2012 20:34:02 ban" -Last Update: "Feb 27 2012 20:34:02 ban" +Created : "2019-05-16 14:48:15 ban" +Last Update: "2019-05-16 14:48:24 ban" ****************************** -The files & data in this directory are sample scripts to run pRF analysis in BrainVoyager +The files in this directory are for running pRF and phase-encoded analyses in BrainVoyager (BrainInnovation, Inc). diff --git a/pRF/olt/pRF_corr_BVQX_hbtools.olt b/pRF/olt/pRF_corr_BVQX_hbtools.olt new file mode 100644 index 0000000..aa6a4e3 --- /dev/null +++ b/pRF/olt/pRF_corr_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 255 0 0 +Color2: 255 29 0 +Color3: 255 57 0 +Color4: 255 85 0 +Color5: 255 114 0 +Color6: 255 142 0 +Color7: 255 170 0 +Color8: 255 199 0 +Color9: 255 227 0 +Color10: 255 255 0 +Color11: 255 0 255 +Color12: 227 0 255 +Color13: 199 0 255 +Color14: 170 0 255 +Color15: 142 0 255 +Color16: 114 0 255 +Color17: 85 0 255 +Color18: 57 0 255 +Color19: 29 0 255 +Color20: 0 0 255 diff --git a/pRF/olt/pRF_eccentricity_BVQX_hbtools.olt b/pRF/olt/pRF_eccentricity_BVQX_hbtools.olt new file mode 100644 index 0000000..1b9a4af --- /dev/null +++ b/pRF/olt/pRF_eccentricity_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 255 54 0 +Color2: 255 227 0 +Color3: 152 255 0 +Color4: 7 255 5 +Color5: 0 255 137 +Color6: 0 245 255 +Color7: 0 100 255 +Color8: 23 0 255 +Color9: 189 0 255 +Color10: 255 0 203 +Color11: 255 54 0 +Color12: 255 227 0 +Color13: 152 255 0 +Color14: 7 255 5 +Color15: 0 255 137 +Color16: 0 245 255 +Color17: 0 100 255 +Color18: 23 0 255 +Color19: 189 0 255 +Color20: 255 0 203 diff --git a/pRF/olt/pRF_hot_cool_BVQX_hbtools.olt b/pRF/olt/pRF_hot_cool_BVQX_hbtools.olt new file mode 100644 index 0000000..86938b0 --- /dev/null +++ b/pRF/olt/pRF_hot_cool_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 255 0 0 +Color2: 255 29 0 +Color3: 255 57 0 +Color4: 255 85 0 +Color5: 255 114 0 +Color6: 255 142 0 +Color7: 255 170 0 +Color8: 255 199 0 +Color9: 255 227 0 +Color10: 255 255 0 +Color11: 0 0 255 +Color12: 0 29 255 +Color13: 0 57 255 +Color14: 0 85 255 +Color15: 0 114 255 +Color16: 0 142 255 +Color17: 0 170 255 +Color18: 0 199 255 +Color19: 0 227 255 +Color20: 0 255 255 diff --git a/pRF/olt/pRF_polar_BVQX_hbtools.olt b/pRF/olt/pRF_polar_BVQX_hbtools.olt new file mode 100644 index 0000000..91062f1 --- /dev/null +++ b/pRF/olt/pRF_polar_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 0 246 252 +Color2: 0 99 255 +Color3: 24 0 255 +Color4: 190 0 255 +Color5: 255 0 200 +Color6: 255 0 200 +Color7: 190 0 255 +Color8: 24 0 255 +Color9: 0 99 255 +Color10: 0 245 255 +Color11: 0 255 138 +Color12: 7 255 5 +Color13: 154 255 0 +Color14: 255 227 0 +Color15: 255 53 0 +Color16: 255 53 0 +Color17: 255 227 0 +Color18: 154 255 0 +Color19: 7 255 6 +Color20: 0 255 142 diff --git a/pRF/olt/pRF_sigma_BVQX_hbtools.olt b/pRF/olt/pRF_sigma_BVQX_hbtools.olt new file mode 100644 index 0000000..783b2b4 --- /dev/null +++ b/pRF/olt/pRF_sigma_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 15 9 6 +Color2: 48 30 19 +Color3: 80 50 32 +Color4: 112 70 45 +Color5: 144 90 58 +Color6: 176 110 70 +Color7: 208 130 83 +Color8: 240 150 96 +Color9: 255 170 109 +Color10: 255 191 122 +Color11: 15 9 6 +Color12: 48 30 19 +Color13: 80 50 32 +Color14: 112 70 45 +Color15: 144 90 58 +Color16: 176 110 70 +Color17: 208 130 83 +Color18: 240 150 96 +Color19: 255 170 109 +Color20: 255 191 122 diff --git a/pRF/olt/pRF_standard_BVQX_hbtools.olt b/pRF/olt/pRF_standard_BVQX_hbtools.olt new file mode 100644 index 0000000..ff6315e --- /dev/null +++ b/pRF/olt/pRF_standard_BVQX_hbtools.olt @@ -0,0 +1,20 @@ +Color1: 255 75 0 +Color2: 255 95 0 +Color3: 255 115 0 +Color4: 255 135 0 +Color5: 255 155 0 +Color6: 255 175 0 +Color7: 255 195 0 +Color8: 255 215 0 +Color9: 255 235 0 +Color10: 255 255 0 +Color11: 0 75 255 +Color12: 0 95 235 +Color13: 0 115 215 +Color14: 0 135 195 +Color15: 0 155 175 +Color16: 0 175 155 +Color17: 0 195 135 +Color18: 0 215 115 +Color19: 0 235 95 +Color20: 0 255 75 diff --git a/pRF/olt/phase_encoded_colors.olt b/pRF/olt/phase_encoded_colors.olt deleted file mode 100644 index aaea202..0000000 --- a/pRF/olt/phase_encoded_colors.olt +++ /dev/null @@ -1,20 +0,0 @@ -Color1: 255 0 77 -Color2: 255 0 153 -Color3: 255 0 230 -Color4: 204 0 255 -Color5: 128 0 255 -Color6: 51 0 255 -Color7: 0 25 255 -Color8: 0 102 255 -Color9: 0 178 255 -Color10: 0 255 255 -Color11: 255 0 0 -Color12: 255 77 0 -Color13: 255 153 0 -Color14: 255 229 0 -Color15: 204 255 0 -Color16: 128 255 0 -Color17: 51 255 0 -Color18: 0 255 25 -Color19: 0 255 102 -Color20: 0 255 179 diff --git a/pRF/olt/script_generate_OLTs_for_pRF_maps.m b/pRF/olt/script_generate_OLTs_for_pRF_maps.m new file mode 100644 index 0000000..896f8a5 --- /dev/null +++ b/pRF/olt/script_generate_OLTs_for_pRF_maps.m @@ -0,0 +1,130 @@ +% script_generate_OLTs_for_pRF_maps.m +% +% a simple script to generate BrainVoyager color lookup tables (*.olt) +% for visualizing pRF and the other statistical mapping results +% +% +% Created : "2018-08-31 09:47:37 ban" +% Last Update: "2018-09-04 17:14:42 ban" + +cv_hbtools_BVQX_setup(1); + +% constants +nLUT=20; % default #LUT of BrainVoyager + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for pRF eccentricity representation +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +lut_pRF_rho=ceil(255.*imresize(generate_colormap_BrainFactory(360,64,-90,1,0,0,0),[nLUT/2,3])); +%lut_pRF_rho=lut_pRF_rho([3:nLUT/2,1:2],:); +lut_pRF_rho(lut_pRF_rho<0)=0; lut_pRF_rho(lut_pRF_rho>255)=255; +lut_pRF_rho=flip(lut_pRF_rho,1); + +fid=fopen('pRF_eccentricity_BVQX_hbtools.olt','w'); +for ii=1:1:nLUT/2 + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_pRF_rho(ii,1),lut_pRF_rho(ii,2),lut_pRF_rho(ii,3))); +end +for ii=1:1:nLUT/2 + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii+nLUT/2,lut_pRF_rho(ii,1),lut_pRF_rho(ii,2),lut_pRF_rho(ii,3))); +end +fclose(fid); + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for pRF polar-angle representation +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +lut_pol=ceil(255.*imresize(generate_colormap_BrainFactory(360,64,0,2,0,0,0),[nLUT,3])); +lut_pol(lut_pol<0)=0; lut_pol(lut_pol>255)=255; + +fid=fopen('pRF_polar_BVQX_hbtools.olt','w'); +for ii=1:1:size(lut_pol,1) + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_pol(ii,1),lut_pol(ii,2),lut_pol(ii,3))); +end +fclose(fid); + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for amplitude etc (hot_cool) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +lut_hot=zeros(nLUT,3); +lut_hot(1:1:nLUT/2,1)=255; +lut_hot(1:1:nLUT/2,2)=ceil(linspace(0,255,nLUT/2)); +lut_hot(1:1:nLUT/2,3)=0; +lut_hot(nLUT/2+1:1:nLUT,1)=0; +lut_hot(nLUT/2+1:1:nLUT,2)=ceil(linspace(0,255,nLUT/2)); +lut_hot(nLUT/2+1:1:nLUT,3)=255; + +fid=fopen('pRF_hot_cool_BVQX_hbtools.olt','w'); +for ii=1:1:size(lut_hot,1) + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_hot(ii,1),lut_hot(ii,2),lut_hot(ii,3))); +end +fclose(fid); + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for correlation etc +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%lut_corr=load(fullfile(fileparts(mfilename('fullpath')),'..','lut','corr.lut')); +%lut_corr=ceil(255.*imresize(lut_corr(:,1:3),[nLUT,3])); +%lut_corr(lut_corr<0)=0; lut_corr(lut_corr>255)=255; + +lut_corr(1:1:nLUT/2,1:3)=ceil([255*ones(nLUT/2,1),linspace(0,255,nLUT/2)',zeros(nLUT/2,1)]); +lut_corr(nLUT/2+1:1:nLUT,1:3)=ceil([linspace(255,0,nLUT/2)',zeros(nLUT/2,1),255*ones(nLUT/2,1)]); +lut_corr(lut_corr<0)=0; lut_corr(lut_corr>255)=255; + +fid=fopen('pRF_corr_BVQX_hbtools.olt','w'); +for ii=1:1:size(lut_corr,1) + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_corr(ii,1),lut_corr(ii,2),lut_corr(ii,3))); +end +fclose(fid); + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for sigma +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +lut_sigma=load(fullfile(fileparts(mfilename('fullpath')),'..','lut','sigma.lut')); +lut_sigma=ceil(255.*imresize(lut_sigma(:,1:3),[nLUT/2,3])); +lut_sigma(lut_sigma<0)=0; lut_sigma(lut_sigma>255)=255; +%lut_sigma(nLUT/2+1:nLUT,:)=lut_sigma(nLUT/2:-1:1,:); +lut_sigma=[lut_sigma;lut_sigma]; + +fid=fopen('pRF_sigma_BVQX_hbtools.olt','w'); +for ii=1:1:size(lut_sigma,1) + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_sigma(ii,1),lut_sigma(ii,2),lut_sigma(ii,3))); +end +fclose(fid); + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% colormap for standard maps (BrainVoyager default) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +lut_standard=[ +255 75 0; +255 95 0; +255 115 0; +255 135 0; +255 155 0; +255 175 0; +255 195 0; +255 215 0; +255 235 0; +255 255 0; +0 75 255; +0 95 235; +0 115 215; +0 135 195; +0 155 175; +0 175 155; +0 195 135; +0 215 115; +0 235 95; +0 255 75]; + +fid=fopen('pRF_standard_BVQX_hbtools.olt','w'); +for ii=1:1:size(lut_standard,1) + fprintf(fid,sprintf('Color%d: % 3d % 3d % 3d\n',ii,lut_standard(ii,1),lut_standard(ii,2),lut_standard(ii,3))); +end +fclose(fid); + +cv_hbtools_BVQX_setup(0); diff --git a/pRF/prt/bar.prt b/pRF/prt/bar.prt new file mode 100644 index 0000000..61dffe3 --- /dev/null +++ b/pRF/prt/bar.prt @@ -0,0 +1,70 @@ + +FileVersion: 2 + +ResolutionOfTime: Volumes + +Experiment: pRF bar + +BackgroundColor: 0 0 0 +TextColor: 255 255 255 +TimeCourseColor: 192 192 192 +TimeCourseThick: 2 +ReferenceFuncColor: 0 0 80 +ReferenceFuncThick: 2 + +NrOfConditions: 9 + +Fix +10 + 1 2 + 19 22 + 39 42 + 59 62 + 79 82 + 99 102 + 119 122 + 139 142 + 159 162 + 179 184 +Color: 195 195 195 + +stim1 +2 + 3 18 + 163 178 +Color: 255 0 191 + +stim2 +1 + 23 38 +Color: 127 0 255 + +stim3 +1 + 43 58 +Color: 0 63 255 + +stim4 +1 + 63 78 +Color: 0 255 255 + +stim5 +1 + 83 98 +Color: 0 255 63 + +stim6 +1 + 103 118 +Color: 127 255 0 + +stim7 +1 + 123 138 +Color: 255 191 0 + +stim8 +1 + 143 158 +Color: 255 0 0 diff --git a/pRF/rtc/bar.rtc b/pRF/rtc/bar.rtc new file mode 100644 index 0000000..134f29d --- /dev/null +++ b/pRF/rtc/bar.rtc @@ -0,0 +1,214 @@ +FileVersion: 2 +Type: DesignMatrix +NrOfPredictors: 9 +NrOfDataPoints: 208 + +"Fix" "stim1" "stim2" "stim3" "stim4" "stim5" "stim6" "stim7" "stim8" +0.003554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.113691 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.457342 0.003554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.717560 0.113691 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.589906 0.460896 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.301949 0.831251 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.087565 1.050803 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +-0.023344 1.133200 0.000000 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