changes before testing

ExptWrapper_Display.m

@@ -0,0 +1,88 @@
+%exptDir = '~/code/rtAttenPenn/';
+%cd(exptDir)
+subjectNum = 500;
+projectName = 'rtAttenPenn';
+Screen('Preference', 'SkipSyncTests', 1);
+subjectRun = 1;
+% **** types of stimuli to train/show to subjects *******
+NEUTRAL = 1;
+SAD = 2;
+HAPPY = 3;
+% *******************************************************
+typeNum = SAD;
+
+subjectName = [datestr(now,5) datestr(now,7) datestr(now,11) num2str(subjectRun) '_' projectName];
+matchNum = 0;
+useButtonBox=1;
+realtimeData = 0;
+debug=1;
+KbName('UnifyKeyNames')
+addpath(genpath('/opt/psychtoolbox/'))
+
+% well the git is set to ignore the data folder so it would just make sense
+% to save here
+% 
+%%
+runNum=2;
+fMRI = 0;
+% today's scanning number
+realtimeData = 0
+debug = 0
+useButtonBox = 0
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+runNum=1;
+fMRI = 6;
+fMRI = 0;
+
+
+%%
+runNum=6;
+fMRI = 16;
+useButtonBox = 1
+realtimeData = 1
+debug = 1
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+runNum = 3;
+fMRI = 14;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+runNum = 4;
+fMRI = 16;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+runNum = 5;
+fMRI = 18;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+%%
+runNum = 6;
+fMRI = 20;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+
+runNum = 7;
+fMRI = 20;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+
+runNum = 8;
+fMRI = 22;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)
+
+
+%%
+
+runNum = 9;
+fMRI = 24;
+[blockData] = RealTimePunisherDisplay(subjectNum,subjectName,matchNum,runNum,useButtonBox,fMRI,realtimeData,debug)

ExptWrapper_FileProcess_Subject1.m → ExptWrapper_FileProcess.m

@@ -9,7 +9,7 @@
 
 %%
 %conf = loadjson('conf/example.json');
-subjectNum = 200;
+subjectNum = 500;
 projectName = 'rtAttenPenn';
 %imgDirHeader = conf.imgDirHeader;
 subjectRun = 1;
@@ -29,7 +29,7 @@
 KbName('UnifyKeyNames')
 
 addpath(genpath('/opt/psychtoolbox/'))
-imgDirHeader = '/Data1/subjects/'
+imgDirHeader = '/Data1/subjects/';
 %% Generate expt sequence
 
 if matchNum ==0

ProcessMask.m

@@ -30,15 +30,15 @@
 end
 
 setenv('FSLOUTPUTTYPE','NIFTI_GZ');
-
+base_path = pwd;
 if matchNum == 0
-    save_dir = ['./data/' num2str(subjectNum)];
+    save_dir = fullfile(pwd,['data/' num2str(subjectNum)]);
 else
-    save_dir = ['./data/' num2str(matchNum) '_match'];
+    save_dir = fullfile(pwd,['data/' num2str(matchNum) '_match']);
 end
 subjectName = [datestr(now,5) datestr(now,7) datestr(now,11) num2str(runNum) '_' projectName];
 dicom_dir = ['/mnt/rtexport/RTexport_Current/' datestr(subjDate,10) datestr(subjDate,5) datestr(subjDate,7) '.' subjectName '.' subjectName '/'];
-process_dir = [save_dir 'reg' '/'];
+process_dir = fullfile(save_dir,[ 'reg' '/']);
 roi_name = 'wholebrain_mask';
 roi_dir = pwd; % change this path name to wherever you put it on the penn computer!
 code_dir = pwd;
@@ -54,7 +54,7 @@
 highresfiles_genstr = sprintf('%s001_0000%s_0*',dicom_dir,num2str(highresScan,'%2.2i')); %general string for ALL mprage files**
 unix(sprintf('%sdicom2bxh %s %s.bxh',bxhpath,highresfiles_genstr,highresFN));
 unix(sprintf('%sbxhreorient --orientation=LAS %s.bxh %s.bxh',bxhpath,highresFN,highresFN_RE));
-unix(sprintf('%sbxh2analyze --overwrite --analyzetypes --niigz --2niftihdr -s %s.bxh %s',bxhpath,highresFN_RE,highresFN_RE))
+unix(sprintf('%sbxh2analyze --overwrite --analyzetypes --niigz --niftihdr -s %s.bxh %s',bxhpath,highresFN_RE,highresFN_RE))
 unix(sprintf('%sbet %s.nii.gz %s_brain.nii.gz -R -m',fslpath,highresFN_RE,highresFN_RE)) 
 %unix(sprintf('%sbet %s.nii.gz %s_brain.nii.gz -r 90 -R',fslpath,highresFN_RE,highresFN_RE)) 
 
@@ -173,9 +173,9 @@
 mask=mask_brain;
 %save anatomical mask
 if matchNum == 0
-    save(['./data/' num2str(subjectNum) '/mask_' num2str(subjectNum)],'mask');
+    save(fullfile(save_dir, [ '/mask_' num2str(subjectNum)]),'mask');
 else
-    save(['./data/' num2str(matchNum) '_match/mask_' num2str(subjectNum)],'mask');
+    save(fullfile(save_dir, [ '/mask_' num2str(subjectNum)]),'mask');
 end
 
 fprintf('Done with mask creation\n');