'''THIS IS A WORK IN PROGRESS AND LIKELY HAS MISTAKES. PLEASE IGNORE FOR NOW'''

BR

FS-FAST USE CASE 1: fMRI Workflow for Reasoning Study

Experiment design

The experiment consists of 3 active conditions (+baseline), referred to as V, T and P.BR The task consists in solving visually presented problems in each of these conditions. Subjects respond using a button box.BR The paradigm is presented in 6 consecutive runs, each lasting 300s. In each run, two of the three conditions are shown to minimize subject confusion, and increase statistical power**WHAT ARE THE EFFECTS ON POWER OF SHOWING ONLY A SUBSET OF THE CONDITIONS IN EACH RUN??. The runs consist of BR Run 1: T-P BR Run 2: T-V BR Run 3: P-V BR Run 4: T-P BR Run 5: T-V BR Run 6: P-V BR This alternation allows for similar scanner drift effects across the different pairings of the conditions (i.e. tentatively the same “amount” of drift occurs between runs 1 and 4 and 2 and 5, assuming drift is linear). Within each run, the plates are presented using a pseudo-randomized (order the same for all subjects, but only known to the experimenter) event-related paradigm. Each plate presentation is considered an event, which can last between 1 and 10s, as the plate disappears when the subject responds or times out after 10 seconds (at which point the paradigm goes on by itself). In-between plates, a fixation cross is shown with a random ISI ranging from 1500 to 3500ms in 250ms steps. Every 6 plates, the fixation cross is held for a longer time, in order to match the total run duration across subjects**IS THIS NECESSARY? WHY? IS THERE A BETTER WAY TO GO ABOUT IT THAN MY 'catchup times'?. Thus, the 7th plate appears at t=75s, the 13th at t=150s and the 19th at t=225s. The total run time of 5minutes is therefore the same as if all plates timed out (10x24 + 2.5x24 = 300). BR The PAR files look like this: BR

Init_time

condition_nb

duration

condition_name

0

0

2.5178

baseline

2.5178

2

2.3427

perceptual

4.8605

0

3.2763

baseline

8.1368

3

2.1638

verbal

10.3006

0

2.5216

baseline

12.8222

2

2.5746

perceptual

15.3968

0

2.0273

baseline

Unpacking

nmrenv BR setenv SUBJECTS_DIR /space/tango/5/users/cherif/reasoning BR findsession <subjID> BR

unpacksdcmdir –src <> -targ <> -scanonly file BR unpacksdcmdir –src <> -targ <subjdir> -fsfast -run <#> bold bshort f -run … (for all 6 runs) BR unpacksdcmdir –src <> -targ <subjdir> -run <#> 3danat cor blah (for the structural) BR

Structural Processing

nmrenvBR setenv SUBJECTS_DIR /space/tango/3/users/recon_modygp/cherif BR recon-all –subjid <subjid> –autorecon1 –autorecon2 BR #perform manual edits BR recon-all –subjid <subjid> -autorecon3 BR

Functional Analysis Stream

cd /space/tango/5/users/cherif/reasoning/ BR ln –s /space/tango/3/users/recon_modygp/cherif/<subjID> <subjID> BR

cd fMRI_analysis/subjects/<subjID> BR cat > fMRI_analysis/subjects/<subjID>/subjectname BR <subjID> BR <ctrl+d> BR

cp <subjid>_run<#>_par.txt bold/<correspondingrun#>/<subjid>_par.par BR cp <subjid>_par.par reason_par.par BR

Pre-porcessing

cd ../ BR preproc-sess –s <subjid> –smout <smfmc#> -fwhm <fwhm> BR **DO YOU STILL WANT TO APPLYS SMOOTHING HERE IF YOU'RE GONNA SMOOTH ON THE SURFACE? SHOULD THERE BE A QUANTITATIVE LINK BETWEEN THE TWO FWHM? BR

Registration to high res scan

spmregister-sess –s <subjid> BR tkregister-sess –s <subjid> BR

Define the analysis: BR mkanalysis-sess.new -analysis reasoning-analysis –TR 2 –paradigm reason_par.par -designtype event-related –funcstem fmcsm5 –nconditions 3 -gammafit 2.25 1.25 –inorm –mcextreg BR **WHAT ARE THE EFFECTS OF CHANGING TAUMAX, TIMEWINDOW, POLYFIT? RULES OF THUMB? HOW TO USE TER? BR IF YOU USE FIR ANALYSIS INSTEAD OF GAMMAFIT, THEN NEED TO CHOOSE TIMEWINDOW AND PRESTIM PARAMETERS. RULE OF THUMB IS TIMEWINDOW=16S+LONGEST EVENT+PRESTIM, AND PRESTIM=2TRS BR

selxavg-sess –s <subjid> -analysis reasoning-analysis