Martinos MultiModal Course 2014 Download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mm2014.tar.gz # See what data is in the DICOM folder dcmunpack -src /path/to/dicom/files 1 localizer MR.1.3.12.2.1107.5.2.30.25096.2014050411155563631372733 2 AAScout MR.1.3.12.2.1107.5.2.30.25096.2014050411162569808773093 3 ge_functionals MR.1.3.12.2.1107.5.2.30.25096.2014050411234712705773934 4 ge_functionals MR.1.3.12.2.1107.5.2.30.25096.2014050411294882794085852 5 ge_functionals MR.1.3.12.2.1107.5.2.30.25096.2014050411372479256202737 6 ge_functionals MR.1.3.12.2.1107.5.2.30.25096.2014050411390389690005462 # Convert from DICOM and setup FSFAST directory structure dcmunpack -src /path/to/dicom/files -targ humor \ -run 3 bold nii.gz f.nii.gz \ -run 4 bold nii.gz f.nii.gz \ -run 5 bold nii.gz f.nii.gz \ -run 6 bold nii.gz f.nii.gz # Copy stimulus schedule files (paradigm files) cp humor-001.par humor/bold/003/humor.par cp humor-002.par humor/bold/004/humor.par cp humor-003.par humor/bold/005/humor.par cp humor-004.par humor/bold/006/humor.par # Event Types 0 NULL 1 Congruent 2 Incongruent 3 Funny # Create subjectname file echo "mm2014b-anat" > humor/subjectname FreeSurfer Analysis: recon-all -s mm2014b-anat -all ... # Preprocessing preproc-sess -surface self lhrh -stc siemens -fwhm 7 -mni305 ... 1. Motion Correction (default) 2. Slice timing correcion ("siemens" timing) 3. Register anatomical to functional 4. Sample to "common space" (self lh and rh surface and mni305 volume) 5. Smooth by 7mm FWHM (surface or volume) # Configure first level (time series) analysis mkanalysis-sess -a mainsm7.lh --> Name of the analysis -stc siemens --> Use STC'ed preprocessed results -surface self lh --> Analysis on left hemisphere of subject -fwhm 7 --> Surface smoothed by 7mm -paradigm humor.par --> stimulus schedule -nc 3 --> number of non-NULL conditions -spmhrf 0 --> Use SPM canonical hemodynamic response # Configure first level contrasts mkcontrast-sess -analysis mainsm7.lh -co Cong-vs-Fix -a 1 -c 0 [1 0 0] mkcontrast-sess -analysis mainsm7.lh -co InCong-vs-Fix -a 2 -c 0 [0 1 0] mkcontrast-sess -analysis mainsm7.lh -co Funny-vs-Fix -a 3 -c 0 [0 0 1] mkcontrast-sess -analysis mainsm7.lh -co Cong-vs-InCong -a 1 -c 2 [1 -1 0] mkcontrast-sess -analysis mainsm7.lh -co Cong-vs-Funny -a 1 -c 3 [1 0 -1] mkcontrast-sess -analysis mainsm7.lh -co InCong-vs-Funny -a 2 -c 3 [0 1 -1] # Analyze first level data selxavg3-sess -s humor -a mainsm7.lh # Humor Contrasts 0 Cong-vs-Fix 1 InCong-vs-Fix 2 Funny-vs-Fix 3 Cong-vs-InCong 4 Cong-vs-Funny 5 InCong-vs-Funny # Language Contrasts 0 EngAbs-Fix 1 EngCon-Fix 2 FreAbs-Fix 3 FreCon-Fix 4 EngAbs-FreAbs 5 EngCon-FreCon 6 Eng-Fre 7 Abs-Con 8 Interact # Love Contrasts 0 LP LoverPos-vs-Fix 1 LN LoverNeg-vs-Fix 2 EP EnemyPos-vs-Fix 3 EN EnemyNeg-vs-Fix 4 FP FriendPos-vs-Fix 5 FN FriendPos-vs-Fix 6 L-E Lover-vs-Enemy 7 L-F Lover-vs-Friend 8 L-E Friend-vs-Enemy 9 LP+EN-LN-EP 10 P-N Pos-vs-Neg # Navigation Contrasts 0 AboveBelow-vs-Fix 1 NearFar-vs-Fix 2 AboveBelow-vs-NearFar 3 Instruct-vs-Fix 4 Inst.AB-vs-NF