http://gru.stanford.edu/ 2026-05-15T01:33:45-0700 http://gru.stanford.edu/ http://gru.stanford.edu/lib/tpl/gru/images/favicon.ico text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/eyetracking?rev=1661892030&do=diff Todo... Akshay and I did more testing last night and we've got it down to ~10 minutes per person. Both calibrations were <1 deg offset. Worked with the projector on as well, but we didn't have time to test with the scanner. If we count on our complete setup taking 30 minutes we should be able to start eye tracking in all experiments. Our key learnings were (1) the person in the scanner needs to ensure that the IR light is pointing straight at their left eye (close right eye to check), (… text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/retinotopywinvsus?rev=1661892030&do=diff Retinotopy Winawer vs Us The ready to use protocol and the matlab script are here ~/proj/gru/GRUExpProtocol/gruRetStanfordvsWinawer/ text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/runningthescanner?rev=1661892030&do=diff Display If you are using the projector: * Replace the flat plastic board behind the scanner with the one in the projector closet. * Put the mirror on that board in the square designating its correct position * Turn the projector on by turning on the power strip. If this still doesn’t work, then look at the back of the projector to see if the switch is in the On position. In the control room, change the text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/stanfordtutorial?rev=1661892030&do=diff Stanford: General fMRI Pipeline This page is a repository for all the tutorials relevant to running fMRI analysis at Stanford. Before you can start these tasks you need to set up a number of things for your computer. The list is on the Stanford Info page, but we repeat it here because you really can't do any of the other steps until this is done: text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_correlation?rev=1661892030&do=diff 5. Correlation Analysis Go to Analysis/Correlation Analysis and fill out the information as follows for all the scans. 8. Show correlation analysis on surfaces Now load one of your surface with superimposed correlation analysis and toggle the Overlay from ph to co, then slide the Overlay min to 0.4 for visualizing (though remember to undo that later). text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_dofmricni?rev=1661892030&do=diff 1. Download Files Open Matlab, either through Terminal or as its own application, and run dofmricni and the following will appear. (If Matlab doesn't recognize dofmricni as a function, make sure it's on your current path; addpath(genpath('~/proj')) may work) text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_mlrreconall?rev=1661892030&do=diff Info We use the Freesurfer standard recon-all segmentation, running at 1 mm resolution. We give Freesurfer 0.9mm resolution scans though because their quality is slightly better than the 1 mm scans. Bob believes this may have to do with fat artifacts near the skull. text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_mralign?rev=1661892030&do=diff Alignment Go to your folder: cd ~/data/cohcon/s030020150101, and run mrAlign. Load Canonical Anatomy Select your Canonical Set as Base Anatomy (if this hasn't been done) Load Source Session Anatomy Set Slice and Alpha so that brain is visible text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_retinotopy?rev=1661892030&do=diff Setup At this point you should have already completed segmentation, dofmricni, and mrAlign. See the specific tutorials for those tasks. Set your Plugins (just tick them all) and call mrLoadRet mlrPlugin('altPlugins=1') mrLoadRet and see the following window appear. text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorial_surfs?rev=1661892030&do=diff Import Surfaces Go to your project directory >> mrLoadRet Select Inflated .off File Setup Files Correctly, Check Alignment in 3D Set up your file choices as follows, and you should see this. If the white dots (GM/WM boundary) and yellow dots (GM/other stuff boundary) aren't in the right spots, either you f'd up (ask somebody) or something went wrong with the segmentation. A possible error here is if the segmentation ran on a T1 collected from the 16ch coil. text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorialprf?rev=1661892030&do=diff Go here. <http://gru.stanford.edu/doku.php/mrTools/tutorialsprf> Tutorial pRF If you get this example warning when running the pRF: (pRFFit:checkStimForAverages) !!! Average for Averages:6 component scan 5 does not match stimulus for other scans. If you wish to continue then this will use the stimfile associated with the first scan in the average !!! Do you wish to continue (y/n or a for Yes to all)? text/html 2022-08-30T13:40:30-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/runningfmri/tutorialsretinotopy?rev=1661892030&do=diff Retinotopy analysis in Stanford The ready to use protocol is here: This detailed checklist for the retinotopy in Stanford need to be re-written here. Setup At this point you should have already completed segmentation, dofmricni, and mrAlign. See the specific tutorials for those tasks.