adding details of data acq

2017-18-scanning.md

@@ -0,0 +1,13 @@
+## Scanner - actual numbers from the day (2017/18)
+
+2. **inplane anatomy** - T1w, 2D MPRAGE. 24 slices, inplane voxel size: 1.5 mm, slice thickness 3 mm (same prescription as fMRI data). Matrix size 128 x 128.
+4. **fMRI data** (and all fMRI scans) 2D gradient-echo EPI, TR 1.5s, TE 40ms, FA: 72º, 160 dynamics. Voxel size 3mm isotropic. Matrix size 64 x 64.
+6. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
+
+## Stimulus set-up
+
+- stimuli were presented on a BOLDscreen (CRS Ltd, Rochester, UK) - https://www.crsltd.com/tools-for-functional-imaging/mr-safe-displays/boldscreen-32-lcd-for-fmri/
+- **2018/19 stimulus code:** inspect ``scene_localiser()`` in the ``stimulusCode`` directory. If you can't run the code and get errors, have a lootk at [this clip on youtube](https://www.youtube.com/watch?v=5kSvEO4-HVc) to get an impression.
+- other details have remained the same since the 2017/18 version.
+
+

2018-19-scanning.md

@@ -0,0 +1,7 @@
+## Scanner - actual numbers from the day (2018/19).
+
+2. **inplane anatomy** - T1w, 2D MPRAGE. 24 slices, inplane voxel size: 1.5 mm, slice thickness 3 mm (same prescription as fMRI data). Matrix size 128 x 128.
+4. **fMRI data** (and all fMRI scans) 2D gradient-echo EPI, TR 1.5s, TE 40ms, FA: 72º, *scene localiser scan*: 294 (288+4) dynamics, retinotopy scan: 160 dynamics. Voxel size 3mm isotropic (acquired). Matrix size 64 x 64. **Note: the scanner reconstruction may have changed the "reconstructed voxel size" to something else, for mathematical expediency.** (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)
+6. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
+7. across the subjects we also acquired various other data sets (including **diffusion weighted**, a **T2 weighted** anatomy scan (using multiple echoes), ... but we didn't find time to analyze these in class.
+

2019-20-scanning.md

@@ -0,0 +1,13 @@
+## Scanner - actual numbers from the day (2019/20).
+
+For each of three subjects (``subject-A``, ``subject-B`` and ``subject-C``) we collected 5 scans. The "series" numbers may be slightly different across individuals. but the scans (in order) were the same:
+
+1. **fMRI data** - 2D gradient-echo EPI, TR 2.0s, TE 30ms, multiband factor 2, FA: 80º, ``scene_localiser()`` scan: 192 dynamics. (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)
+
+2. **fMRI data** - acquisition details as in 1, but only 120 dynamics. Pseudorandomly ordered blocks on "normal", "inverted" and "caricatured" faces (at different levels).
+
+3. same as 2 (a repeat)
+
+4. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
+
+5. **T2 weighted** anatomy scan. TE 89ms, TR 3.38s, FA, 90º (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)

2022-23-scanning.md

@@ -0,0 +1,14 @@
+## Scanner - actual numbers from the day (2022/23).
+
+For each of four subjects (``sub-01`` .. ``sub-02``) we collected most of those scans. Look at the `Readme.md` file in each folder for any notes (eg `sub-02` has one scan with TR=2s, because of the sample protocol I had picked.) 
+
+Data shared via `OneDrive` link on a moodle message to the participants on the module.
+
+### A note on the block-design parameters.
+
+- the visual scan (faces versus objects) used a `rest-A-rest-B-...` pattern.
+- the finger tapping scan follwed the same timing. `rest-LEFT-rest-RIGHT...`
+
+Each `rest-stimulus` block took 24s (so 16 TRs at 1.5s... or 12 TRs for the one scan with a 2s TR).
+
+The code for these experiments is in the `stimulusCode` folder (`FFAlocaliser()` and `M1localiser()`). Ask DS for details on how this works, if you are interested in generating stimuli.

gettingData.md

@@ -24,90 +24,116 @@ The protocol will be pretty standard for a cognitive neuroscience scanning sessi
 2. A test EPI to make sure that the slice positioning for the fMRI experiment is ok.
 3. fMRI experiment (block): gradient-echo EPI, TR 1.5s **(~4min)**
 4. T1w-MPRAGE: to illustrate detailed (1mm isotropic) anatomy **(~5min)**
-5. T2w-anatomy: higher resolution inplane, but thicker slices
-6. fMRI experiment (block): gradient-echo EPI, TR 1.5s **(~4min)** (a finger-tapping experiment as opposed to a visual experiment)
+5. T2w-FLAIR: (1mm isotropic)
 
-## Scanner - actual numbers from the day (2023/24).
+## Stimulus code 
 
-*details to be updated*
++ stimulus code: inspect ``FFAlocaliser``  for lots of details. 
++ **timing: block design** 12s images (faces, objects), 12s rest: a 24s cycle. 10 repeats per scan - 240s or 160 dynamics (@ 1.5s). Stimuli were images from face and object image database (details below).
 
+The code is written in ``matlab/mgl`` using the ``task`` library that comes with ``mgl``. Written by Alex Beckett and DS based on a version of a working code from Justin Gardner :smile:
 
-## Scanner - actual numbers from the day (2022/23).
+There are a couple of short youtube videos explaining a version of <a href="https://youtu.be/wcA_h-rrVeM" target="_blank">the FFA localiser</a> and the <a href="https://youtu.be/exqNc7q8zSs" target="_blank">fixation dimming task</a> to control attention, which would be used in a real experiment. This should give you  a sense of what the subject is doing inside the scanner.
 
-For each of four subjects (``sub-01`` .. ``sub-02``) we collected most of those scans. Look at the `Readme.md` file in each folder for any notes (eg `sub-02` has one scan with TR=2s, because of the sample protocol I had picked.) 
+The experiment runs as a simple block design in the following order:
 
-Data shared via `OneDrive` link on a moodle message to the participants on the module.
+>[faces, rest] , [objects, rest] - ...
 
-### A note on the block-design parameters.
+The length of each ``[stimulus, rest]`` cycle is determined by the ``cycleLength`` (in TRs).
 
-- the visual scan (faces versus objects) used a `rest-A-rest-B-...` pattern.
-- the finger tapping scan follwed the same timing. `rest-LEFT-rest-RIGHT...`
+To run, make sure the ``stimulusCode`` folder is on the path and then simply run the following command. the ``Escape`` key can be used to stop the experiment at any point:
 
-Each `rest-stimulus` block took 24s (so 16 TRs at 1.5s... or 12 TRs for the one scan with a 2s TR).
+```matlab
+FFAlocaliser % quick test to see what's going on
+```
 
-The code for these experiments is in the `stimulusCode` folder (`FFAlocaliser()` and `M1localiser()`). Ask DS for details on how this works, if you are interested in generating stimuli.
+To run at the MR centre, we also want to specify TR, not to run in a small window, etc. So probably worth setting a few parameters in the call like this:
 
-## Scanner - actual numbers from the day (2019/20).
+```matlab
+FFAlocaliser('TR=1.5', 'debug=0', 'numBlocks=10', 'cycleLength=12')
+```
 
-For each of three subjects (``subject-A``, ``subject-B`` and ``subject-C``) we collected 5 scans. The "series" numbers may be slightly different across individuals. but the scans (in order) were the same:
+## Scanner - actual numbers from the day (2023/24)
 
-1. **fMRI data** - 2D gradient-echo EPI, TR 2.0s, TE 30ms, multiband factor 2, FA: 80º, ``scene_localiser()`` scan: 192 dynamics. (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)
+2024-02-07, Denis Schluppeck
 
-2. **fMRI data** - acquisition details as in 1, but only 120 dynamics. Pseudorandomly ordered blocks on "normal", "inverted" and "caricatured" faces (at different levels).
+4 volunteers (``sub-01`` .. ``sub-04``), scanned on the 3T GE scanner at the SPMIC QMC site. Scanner operator: AC. Start time 1400h.
 
-3. same as 2 (a repeat)
+(Data available via `moodle` link to a zip file on OneDrive). 
 
-4. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
+For each person we obtained several scans. See `json` sidecar copied along for some details.
 
-5. **T2 weighted** anatomy scan. TE 89ms, TR 3.38s, FA, 90º (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)
+- T1w MPRAGE (1mm isotropic)
+- T2w FLAIR  (1mm isotropic)
+- one or two repeats of an fMRI experiment (`FFAlocaliser.m`); 2.2mm isotropic, TR/TE 1500ms/35ms
 
-## Scanner - actual numbers from the day (2018/19).
+## fMRI experiment and timing
 
-2. **inplane anatomy** - T1w, 2D MPRAGE. 24 slices, inplane voxel size: 1.5 mm, slice thickness 3 mm (same prescription as fMRI data). Matrix size 128 x 128.
-4. **fMRI data** (and all fMRI scans) 2D gradient-echo EPI, TR 1.5s, TE 40ms, FA: 72º, *scene localiser scan*: 294 (288+4) dynamics, retinotopy scan: 160 dynamics. Voxel size 3mm isotropic (acquired). Matrix size 64 x 64. **Note: the scanner reconstruction may have changed the "reconstructed voxel size" to something else, for mathematical expediency.** (Check the dimensions in the actual data with ``fslinfo`` or ``fslhd``.)
-6. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
-7. across the subjects we also acquired various other data sets (including **diffusion weighted**, a **T2 weighted** anatomy scan (using multiple echoes), ... but we didn't find time to analyze these in class.
+- the original scan was 168 timepoints long, but the first 8TRs (12s) were cut to allow for steady state. 
+- after removing these initial dummies, the time series is 160 timepoints long
+- timing of the experiment is (Faces-rest-Obj-rest)*5)
 
-## Scanner - actual numbers from the day (2017/18)
+```
+12s ON (faces)
+12s OFF (gray)
 
-2. **inplane anatomy** - T1w, 2D MPRAGE. 24 slices, inplane voxel size: 1.5 mm, slice thickness 3 mm (same prescription as fMRI data). Matrix size 128 x 128.
-4. **fMRI data** (and all fMRI scans) 2D gradient-echo EPI, TR 1.5s, TE 40ms, FA: 72º, 160 dynamics. Voxel size 3mm isotropic. Matrix size 64 x 64.
-6. **whole head anatomy** - T1w 3D MPRAGE. Matrix size 256 x 256, 160 slices. Reconstructed as sagittal images. voxel size 1 mm isotropic. TE 3.7 ms, TR 8.13 ms, FA 8°, TI 960 ms, and linear phase encoding order.
+12s ON (objects)
+12s OFF (gray)
 
-## Stimulus set-up
+... then each repeated for a total of 10 stimulus-rest blocks 
+```
 
-- stimuli were presented on a BOLDscreen (CRS Ltd, Rochester, UK) - https://www.crsltd.com/tools-for-functional-imaging/mr-safe-displays/boldscreen-32-lcd-for-fmri/
-- **2018/19 stimulus code:** inspect ``scene_localiser()`` in the ``stimulusCode`` directory. If you can't run the code and get errors, have a lootk at [this clip on youtube](https://www.youtube.com/watch?v=5kSvEO4-HVc) to get an impression.
-- other details have remained the same since the 2017/18 version.
+## File organisation 
+
+The zip file contains data from the 4 participants in the following layout:
+
+```text
+.
+├── Readme.md
+├── sub-01
+├── sub-02
+│   ├── sub-02-FLAIR.png
+│   ├── sub-02-MPRAGE.png
+│   ├── sub-02-flair.json
+│   ├── sub-02-flair.nii.gz
+│   ├── sub-02-fmri01.nii.gz
+│   ├── sub-02-fmri02.nii.gz
+│   ├── sub-02-mprage.json
+│   └── sub-02-mprage.nii.gz
+├── sub-03
+└── sub-04
 
+```
 
-## Stimulus code (2017/18)
 
-+ stimulus code: inspect ``FFAlocaliser`` and ``jazLocaliser`` for lots of details. You should be able to run the code, too.
-+ **timing: block design** 12s rest, 12s images (faces, objects), so 24s cycles. 10 repeats per scan - 240s or 160 dynamics (@ 1.5s). Stimuli were images from face and object image database (details below).
-+ **timing: event-related design** 1.5s stimuli followed be a randomly chosen ITI between 9s and and 18s (in 1.5s increments). Stimuli were white, moving, random dots on a black background. 100% coherence, speed 4 deg/s. Scans lasted 240s or 160 dynamics (@ 1.5s).
+## Notes
 
-The code is written in ``matlab/mgl`` using the ``task`` library that comes with ``mgl``. Written by Alex Beckett and DS based on a version of a working code from Justin Gardner :smile:
+For FSL design matrix rules, this means for EVs
 
-There are a couple of short youtube videos explaining <a href="https://youtu.be/wcA_h-rrVeM" target="_blank">the FFA localiser</a> and the <a href="https://youtu.be/exqNc7q8zSs" target="_blank">fixation dimming task</a> to control attention. This should give you  a sense of what the subject is doing inside the scanner.
+| setting     | Faces  | Objects |
+| :---------- | :----- | :------ |
+| Skip        | 36     | 36      |
+| Off         | 36     | 36      |
+| On          | 12     | 12      |
+| Phase       | **36** | **12**  |
+| Stop After  | -1     | -1      |
+| Convolution | Gamma  | Gamma   |
 
-The experiment runs as a simple block design in the following order:
 
->[faces, rest] , [objects, rest] - ...
 
-The length of each ``[stimulus, rest]`` cycle is determined by the ``cycleLength`` (in TRs).
 
-To run, make sure the ``stimulusCode`` folder is on the path and then simply run the following command. the ``Escape`` key can be used to stop the experiment at any point:
 
-```Matlab
-FFAlocaliser % quick test to see what's going on
-```
+## Previous scanning sessions
+
+- [2022-23 cohort](./2022-23-scanning.md)
+
+- [2019-20 cohort](./2019-20-scanning.md)
+
+- [2018-19 cohort](./2018-19-scanning.md)
+
+- [2017-18 cohort](./2017-18-scanning.md)
 
-To run at the MR centre, we also want to specify TR, not to run in a small window, etc. So probably worth setting a few parameters in the call like this:
 
-```Matlab
-FFAlocaliser('TR=1.5', 'debug=0', 'numBlocks=10', 'cycleLength=12')
-```
 
 ### Notes
 

stimulusCode/FFAlocaliser.m

@@ -6,8 +6,13 @@
 %    purpose: code for doing face and object area localiser.
 %             images courtesy of Tim Andrews (York) and others.
 %
+%             
+%
+%             
+%
 %       e.g.:
 %             FFAlocaliser()
+%             FFAlocaliser('displayname=3T-GE-debug', 'TR=1.5')
 %
 % make sure to also look at jazLocaliser.m for event-related expt
 function myscreen = FFAlocaliser( varargin )
@@ -17,6 +22,8 @@
 
 % setup default arguments
 if ieNotDefined('debug'), debug=0; end
+if ieNotDefined('displayname'), displayname = ''; end
+
 
 % scanning params
 if ieNotDefined('TR'), TR=1.5; end
@@ -50,7 +57,7 @@
 myscreen.datadir = './';
 myscreen.allowpause = 0;
 myscreen.eatkeys = 1;
-myscreen.displayname = '';
+myscreen.displayname = displayname;
 myscreen.background = 'gray';
 myscreen.TR = TR;
 myscreen.cycleLength = cycleLength; % in TRs
@@ -65,6 +72,7 @@
 fixStimulus.diskSize = 0.0; % no disk (just superimpose on stim)
 fixStimulus.fixWidth = 1;
 
+% by default the screen params should come from mglEditScreenParams setup!!
 if debug == 1
   % gethostname and then display the stimulus on the corresponding screen
   % myscreen.screenParams{1} = {gethostname(),[],0,1024,768,80,[31 23],60,1,1,1.4,[],flipHV};
@@ -79,23 +87,25 @@
   fixStimulus.fixWidth = 1; 
   fixStimulus.diskSize = 0; 
 
-else    
-  % running at 3T for experiment
-  defaultMonitorGamma = 1.8;
-  % myscreen.screenParams{1} = {gethostname(),'',2,1280,960,231,[83 3*83/4],60,1,1,defaultMonitorGamma,'',flipHV}; % 3T nottingham
-    myscreen.screenParams{1} = struct('computerName', gethostname(),...
-            'displayName',[], 'screenNumber', 2, ...
-		    'screenWidth', 1280, 'screenHeight', 960, 'displayDistance', 231,...
-		    'displaySize',[83 3*83/4], 'framesPerSecond', 60, 'autoCloseScreen', 1, ...
-		    'saveData', 1, 'calibType', 1, 'monitorGamma', defaultMonitorGamma, 'calibFilename',[], ...
-		    'flipHV', flipHV, 'digin',[],  'hideCursor', 1, 'displayPos', [],  'backtickChar', '5');
+elseif debug == 2 
+    fprintf('should not need this code!!')
+    % don't run this code now...     
+    % running at 3T for experiment
+    %   defaultMonitorGamma = 1.8;
+    %   % myscreen.screenParams{1} = {gethostname(),'',2,1280,960,231,[83 3*83/4],60,1,1,defaultMonitorGamma,'',flipHV}; % 3T nottingham
+    %     myscreen.screenParams{1} = struct('computerName', gethostname(),...
+    %             'displayName',displayname, 'screenNumber', 2, ...
+    % 		    'screenWidth', 1280, 'screenHeight', 960, 'displayDistance', 231,...
+    % 		    'displaySize',[83 3*83/4], 'framesPerSecond', 60, 'autoCloseScreen', 1, ...
+    % 		    'saveData', 1, 'calibType', 1, 'monitorGamma', defaultMonitorGamma, 'calibFilename',[], ...
+    % 		    'flipHV', flipHV, 'digin',[],  'hideCursor', 1, 'displayPos', [],  'backtickChar', '5');
 end
 
 % and init myscreen
 myscreen = initScreen(myscreen);
 
 % fix keys for our scanner setup.
-myscreen.keyboard.backtick = mglCharToKeycode({'5'}); % that's the backtick
+% myscreen.keyboard.backtick = mglCharToKeycode({'5'}); % that's the backtick
 myscreen.keyboard.nums = mglCharToKeycode({'1' '2' '3' '4'    '6' '7' '8' '9' '0'});
 
 % set the first task to be the fixation staircase task
@@ -132,7 +142,7 @@
 myscreen = initStimulus('stimulus',myscreen);
 % load in images and prep textures
 stimulus = initFaces(stimulus,myscreen);
-stimulus.displayWidth = 10; % decide how WIDE the stimuli should be
+stimulus.displayWidth = 18; %  WAS 10!! decide how WIDE the stimuli should be
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % run the eye calibration
@@ -249,12 +259,14 @@
 MAX_IMAGES_TO_LOAD = 50;
 
 % stim directories are hard-coded. Could do better here.
-imdir{1} = './stims/multiracial/frontal/';
-files{1} = dir([imdir{1} '*.jpg']);
+% imdir{1} = './stims/multiracial/frontal/';
+imdir{1} = './scene_localiser/images/';
+files{1} = dir([imdir{1} 'face_*.png']);
 nFiles{1} = min(MAX_IMAGES_TO_LOAD, length(files{1}));
 
-imdir{2} = './stims/objects/';
-files{2} = dir([imdir{2} '*.jpg']);
+% imdir{2} = './stims/objects/';
+imdir{2} ='./scene_localiser/images/';
+files{2} = dir([imdir{2} 'object*.png']);
 nFiles{2} = min(MAX_IMAGES_TO_LOAD, length(files{2}));
 
 % imdir{3} = './stims/houses/';
@@ -274,7 +286,7 @@
       im2 = reshape(im, imdims(1).*imdims(2), []); % x*y, RGBA
       im2(:,4) = 255.0; % add transparency layer and also makes it FLOAT!!
 
-      WHITE_CUTOFF = 200;
+      WHITE_CUTOFF = 254;
       GRAY_VAL = 127;
 
       % place on textured noise?