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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]] |
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 [[BR]] '''''**WHAT ARE THE EFFECTS ON POWER OF SHOWING ONLY A SUBSET OF THE CONDITIONS IN EACH RUN??'''''. [[BR]] The runs consist of [[BR]] |
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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]] |
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. [[BR]] '''''**IS THIS NECESSARY? WHY? IS THERE A BETTER WAY TO GO ABOUT IT THAN MY 'catchup times'?'''''. [[BR]] 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]] |
'''THIS IS A WORK IN PROGRESS AND LIKELY HAS MISTAKES. PLEASE IGNORE FOR NOW'''
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 BR **WHAT ARE THE EFFECTS ON POWER OF SHOWING ONLY A SUBSET OF THE CONDITIONS IN EACH RUN??. BR 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. BR **IS THIS NECESSARY? WHY? IS THERE A BETTER WAY TO GO ABOUT IT THAN MY 'catchup times'?. BR 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
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
Run the Analysis
selxavg-sess s <subjid> -analysis reasoning-analysis