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| ='''THIS IS A WORK IN PROGRESS AND LIKELY HAS MISTAKES. PLEASE IGNORE FOR NOW'''= | = '''THIS IS A WORK IN PROGRESS AND LIKELY HAS MISTAKES. PLEASE IGNORE FOR NOW''' = |
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| ==FS-FAST USE CASE 1: fMRI Sorkflow for Reasoning Study== | == FS-FAST USE CASE 1: fMRI Sorkflow for Reasoning Study == |
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| ===Experiment design=== The experiment consists of 3 active conditions (+baseline), referred to as V, T and P. The task consists in solving visually presented problems in each of these conditions. Subjects respond using a button box. 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**. The runs consist of Run 1: T-P Run 2: T-V Run 3: P-V Run 4: T-P Run 5: T-V Run 6: P-V |
=== 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]] |
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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**. 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). The PAR files look like this: 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 |
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 || |
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=== 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 === nmrenv[[BR]] 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]] |
'''THIS IS A WORK IN PROGRESS AND LIKELY HAS MISTAKES. PLEASE IGNORE FOR NOW'''
FS-FAST USE CASE 1: fMRI Sorkflow 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