Faces Experiment Conditions: 1. Famous-RSU (RSU = right-side up) 2. NewlyFamilar-RSU 3. Unfamiliar-RSU 4. Objects-RSU 5. Famous-USD (USD = upside-down) 6. NewlyFamilar-USD 7. Unfamiliar-USD 8. Objects-USD # Optimize stimulus schedule # surfer.nmr.mgh.harvard.edu/optseq optseq2 --ntp 180 --> number of time points --tr 2 --> TR in seconds --psdwin 0 20 --> post-stimulus delay window --ev Famous 2 20 --> 2 sec event repeated 20 times --ev NewlyFamiliar 2 20 --ev UnFamiliar 2 20 --ev Object 2 20 --ev Famous-USD 2 20 --ev NewlyFam-USD 2 20 --ev UnFam-USD 2 20 --ev Object-USD 2 20 --polyfit 2 --> include 2nd order polynomial --focb 100 --> optimize first-order counter-balancing --nsearch 10000 --> search 10000 sequences --nkeep 5 --> save the best 5 runs --o faces --> output will be faces-001.par, faces-002.par,... --------------------------------------------- Example Paradigm file (faces-001.par) OnsetTime StimID Duration Weight StimName - - - - - - - - - - - - - - - - - - - - - - - 0.0000 5 2.000 1.0000 Famous-USD 2.0000 6 2.000 1.0000 NewlyFam-USD 4.0000 0 2.000 1.0000 NULL 6.0000 3 2.000 1.0000 UnFam 8.0000 1 2.000 1.0000 Famous-RSU 10.0000 3 2.000 1.0000 UnFam 12.0000 6 2.000 1.0000 NewlyFam-USD --------------------------------------------- ################################# # Give paradigm files to Alex ################################# ################################# # Collect data at scanner ################################# # Unpack from DICOM files dcmunpack -src /mount/cdrom/dicom \ -targ faces --> name of session folder -run 3 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii # Creates: faces/bold/003/f.nii faces/bold/005/f.nii faces/bold/006/f.nii faces/bold/007/f.nii faces/bold/008/f.nii # Copy paradigm files to run folder: cp faces-001.par faces/bold/003/faces.par cp faces-002.par faces/bold/005/faces.par cp faces-003.par faces/bold/006/faces.par cp faces-004.par faces/bold/007/faces.par cp faces-005.par faces/bold/008/faces.par # Preprocess: preproc-sess -s faces --> folder where the data are -stc siemens --> slice timing correction using Siemens default slice timging -fwhm 7 --> Smooth by 7mm FWHM # Motion correction is implicit # Performs registration with anatomical # Configure analysis (design matrix) mkanalysis-sess \ -analysis mainsm7 --> Name of analysis -stc siemens --> Use slice timing correction -fwhm 7 --> Use data smoothed by 7mm -paradigm faces.par --> paradigm file -nc 8 --> Number of conditions to expect -spmhrf --> Assume SPM HRF shape -polyfit 2 --> include 2nd order polynomial (nuisance) -nskip 4 --> Skip first 4 time points (nuisance) # Create contrasts mkcontrast-sess -analysis mainsm7 --> Name of analysis -contrast famous-rsu-vs-fix --> Name of contrast -a 1 -c 0 --> Contrast condition 1 vs condition 0 mkcontrast-sess -an mainsm7 -co famous-usd-vs-fix -a 5 -c 0 mkcontrast-sess -an mainsm7 -co obj-rsu-vs-fix -a 4 -c 0 mkcontrast-sess -an mainsm7 -co obj-usd-vs-fix -a 8 -c 0 mkcontrast-sess -an mainsm7 -co faces-vs-obj -a 1 -a 2 -a 3 -c 4 # Visualize results in the volume tkmedit-sess -a mainsm7 \ -c famous-rsu-vs-fix \ -c famous-usd-vs-fix \ -c obj-rsu-vs-fix \ -c obj-usd-vs-fix \ -c faces-vs-obj \ -c famous-vs-unfam \ -c famous-vs-newfam \ -c newfam-vs-unfam \ -c rsu-vs-usd.faces \ -c rsu-vs-usd.obj # Visualize results on the surface tksurfer-sess -cwd -a mainsm7 -self -hemi lh \ -c famous-rsu-vs-fix \ -c famous-usd-vs-fix \ -c obj-rsu-vs-fix \ -c obj-usd-vs-fix \ -c faces-vs-obj \ -c famous-vs-unfam \ -c famous-vs-newfam \ -c newfam-vs-unfam \ -c rsu-vs-usd.faces \ -c rsu-vs-usd.obj Contrasts: 0 Famous-RSU vs Fix 1 Famous-USD 2 Objects-RSU vs Fix 3 Objects-USD vs Fix 4 Faces vs Objects 5 Famous vs Unfamiliar 6 Famous vs Newly Familiar 7 Newly Familiar vs Unfamiliar 8 RSU vs USD Faces 9 RSU vs USD Objects ================================================= Language Experiment Username: nmrclass Password: brain.map (for both decryption and login) Directory: ~/vrfp-oct12/language cd ~/vrfp-oct12/language Create a directory called pics To create a picture run: import pics/Far-Close.sagittal.slice150.gif The cursor turns to a cross, then click on the image you want Contrasts: 0 SpanishSilent vs Fix 1 SpanishAloud vs Fix 2 EnglishSilent vs Fix 3 EnglishAloud vs Fix 4 SpanishAloud vs SpanishSilent 5 EnglishAloud vs EnglishSilent 6 EnglishAloud vs SpanishAloud 7 EnglishSilent vs SpanishSilent 8 (EA-vs-ES) - (SA-vs-SS) tkmedit-sess -cwd -a mainsm7 \ -c SS-vs-fix \ -c SA-vs-fix \ -c ES-vs-fix \ -c EA-vs-fix \ -c SA-vs-SS \ -c EA-vs-ES \ -c EA-vs-SA \ -c ES-vs-SS \ -c EA-vs-ES--SA-vs-SS tksurfer-sess -cwd -a mainsm7 -self -hemi lh\ -c SS-vs-fix \ -c SA-vs-fix \ -c ES-vs-fix \ -c EA-vs-fix \ -c SA-vs-SS \ -c EA-vs-ES \ -c EA-vs-SA \ -c ES-vs-SS \ -c EA-vs-ES--SA-vs-SS tksurfer-sess -cwd -a mainsm7 -self -hemi rh\ -c SS-vs-fix \ -c SA-vs-fix \ -c ES-vs-fix \ -c EA-vs-fix \ -c SA-vs-SS \ -c EA-vs-ES \ -c EA-vs-SA \ -c ES-vs-SS \ -c EA-vs-ES--SA-vs-SS # -------------------------------------------------------------- Conditions: 1. SpanishSilent 2. SpanishAloud 3. EnglishSilent 4. EnglishAloud 5. Instruction preproc-sess -cwd -fwhm 7 -per-session -fsd bold -stc siemens mkanalysis-sess -a mainsm7 -native -fwhm 7 -stc siemens -fsd bold \ -event-related -paradigm lang.par -TR 2 \ -nc 5 -spmhrf 0 -refeventdur 20 -nskip 4 -nowhiten mkcontrast-sess -an mainsm7 -co SS-vs-fix -a 1 -c 0 mkcontrast-sess -an mainsm7 -co SA-vs-fix -a 2 -c 0 mkcontrast-sess -an mainsm7 -co ES-vs-fix -a 3 -c 0 mkcontrast-sess -an mainsm7 -co EA-vs-fix -a 4 -c 0 mkcontrast-sess -an mainsm7 -co SA-vs-SS -a 2 -c 1 mkcontrast-sess -an mainsm7 -co EA-vs-ES -a 4 -c 3 mkcontrast-sess -an mainsm7 -co EA-vs-SA -a 4 -c 2 mkcontrast-sess -an mainsm7 -co ES-vs-SS -a 3 -c 1 mkcontrast-sess -an mainsm7 -co EA-vs-ES--SA-vs-SS -a 4 -c 3 -c 2 -a 1 mkcontrast-sess -an mainsm7 -co Instr-vs-fix -a 5 -c 0