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======Neural similarity for color variation - Design======


=====Stimuli=====

The stimuli run from blue to green in the experimental program configuration files. The following stimulus labels were mapped from the sequence to the stimuli:

^Sequence label^Stimulus^
|0|null-trial (background)|
|1|Blue|
|2|
|3|
|4|
|5|
|6|
|7|
|8|
|9|
|A|Green|

=====Sequence design=====
Given 10 stimuli and a null-trial, a k=11, n=3 de Bruijn sequence (1331 elements) was created using the [[de_bruijn_software|de bruijn cycle software]]. A trial duration of 1100 msecs and a linear adaptation neural model were applied. The sequence was obtained with an iterative approach that searched across 7000 sequences with different guide functions. The resulting sequence, shown below, has most of its power concentrated at the 17th frequency.

<code - NeuralModel.txt>
-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-1 0 1 2 3 4 5 6 7 8 9
-1 1 0 1 2 3 4 5 6 7 8
-1 2 1 0 1 2 3 4 5 6 7
-1 3 2 1 0 1 2 3 4 5 6
-1 4 3 2 1 0 1 2 3 4 5
-1 5 4 3 2 1 0 1 2 3 4
-1 6 5 4 3 2 1 0 1 2 3
-1 7 6 5 4 3 2 1 0 1 2
-1 8 7 6 5 4 3 2 1 0 1
-1 9 8 7 6 5 4 3 2 1 0
</code>


<code - k11n3_ColorAdapt.txt>
7089899A99988870320313235757A851628393A4A49392A19291829382A5A509696353123245665554443332223345434653525263738384A3A2A39191A2928071A48282727302586421343212211120889A08777054557890A8695017294A59271937181A1A3819492617396A7464676542344577886667766446608656579758500183A51A52A281804A27A262A400094848630A987876706688AAA0335567867564534240636941717A4195A1849174A17916185A472840269790341214422055331133663308A9A89764102749401A61A716A372A6295915A304951759625142067990855885468966997755231460358A8A7A6A5826A4619616925A2507268259471595841405325403652244114310303779860568A6024859361504837A36A163A35A693004160952796060AA90570A05210844083378A065895305875285836275A7253946A24A6395710073A6847A75106476879AA884581243560125632674257638A53852968307A5724964A736318A428A2028686A874367A978569A7020A760038942651368536047350297209359714A824186109101681515802364306803A96598A34784376985740A64097AA795480924748178317614973164901524276A650A562463404387A0A43A84690691315379452010A31974157349A54983518931A8348A156A9561301413541A943902154753A78204626075062165A801374793278002A7732891489200A2170110512648733862309098429042A934A923754A0225519006A01982380612709A67218723A104074511559079219A450503970059A1388329A32A8147045996713A099550821AA662078166AA55A912871298107622661177A145AA44774488227722880A12A0449944AA239A229933AA339805A0080813991188119922AA11A0707711673
</code>

^Correlation^Detection Power^
|0.553022|0.557784|

Additional blank ("zero") trials were added to the sequence to increase the power of the main effect (all stimuli vs. null-trials) and to increase the total length of the sequence to 1500 elements (which is an integer multiple of TRs and is divisible into 5 scans).

In summary:

^TRs^seconds^trials^
|550|1650|1500|

====Expanded sequence====

For use in fMRI data collection, each instance of the "zero" label was first doubled. Then, 48 zero labels were randomly selected to be doubled again, resulting in a sequence with 1500 elements:

<code - k11n3_ColorAdapt_ZeroEnhanced_1.0.txt>
700089899A99988870003200313235757A851628393A4A49392A19291829382A5A50009696353123245665554443332223345434653525263738384A3A2A39191A29280071A4828272730025864213432122111200889A000877700545578900A869500017294A59271937181A1A3819492617396A74646765423445778866677664466008656579758500000183A51A52A2818004A27A262A400000000948486300A9878767006688AAA00335567867564534240000636941717A4195A1849174A17916185A47284002697900034121442200553311336633008A9A8976410027494001A61A716A372A6295915A3000495175962514200067990008558854689669977552314600358A8A7A6A5826A4619616925A250072682594715958414005325400036522441143100300377986000568A600248593615004837A36A163A35A69300000416009527960006000AA90057000A00052100844000083378A00658953005875285836275A7253946A24A639571000073A6847A751006476879AA8845812435600125632674257638A538529683007A5724964A736318A428A20028686A874367A978569A700200A7600000389426513685360047350000297200009359714A8241861000091000168151580002364300680003A96598A347843769857400A6400097AA7954800092474817831761497316490001524276A6500A5624634004387A00A43A8469000691315379452001000A31974157349A54983518931A8348A156A95613001413541A9439002154753A78200462600750062165A8001374793278000002A7732891489200000A2170011005126487338623009009842900042A934A923754A00022551900006A001982380061270009A67218723A1004000745115590079219A45005003970000059A1388329A32A814700045996713A00995500821AA6620078166AA55A9128712981007622661177A145AA447744882277228800A12A00449944AA239A229933AA33980005A00000800813991188119922AA11A007007711673</code>

This was then broken into 5 sections of 300 elements (which is an integer multiple of 30 and trials with TRs). Each sub-sequence repeats the last 30 elements from the prior sub-sequence at the onset. This allows the first 11 seconds of each scan to be discarded prior to knitting together the functional data. Each complete sub-sequence is therefore 330 elements, corresponding to 121 TRs. In analysis, the first 11 TRs of each raw DICOM file is discarded, and the resulting 110 TR data files concatenated and modeled with the complete sequence above (plus zero-padding with 48 blank trials at the end).

The resulting sub-sequences are:

|ColorSubSeq_1.txt|<code>3991188119922AA11A007007711673700089899A99988870003200313235757A851628393A4A49392A19291829382A5A50009696353123245665554443332223345434653525263738384A3A2A39191A29280071A4828272730025864213432122111200889A000877700545578900A869500017294A59271937181A1A3819492617396A74646765423445778866677664466008656579758500000183A51A52A2818004A2</code>|
|ColorSubSeq_2.txt|<code>79758500000183A51A52A2818004A27A262A400000000948486300A9878767006688AAA00335567867564534240000636941717A4195A1849174A17916185A47284002697900034121442200553311336633008A9A8976410027494001A61A716A372A6295915A3000495175962514200067990008558854689669977552314600358A8A7A6A5826A4619616925A2500726825947159584140053254000365224411431003</code>|
|ColorSubSeq_3.txt|<code>58414005325400036522441143100300377986000568A600248593615004837A36A163A35A69300000416009527960006000AA90057000A00052100844000083378A00658953005875285836275A7253946A24A639571000073A6847A751006476879AA8845812435600125632674257638A538529683007A5724964A736318A428A20028686A874367A978569A700200A7600000389426513685360047350000297200009</code>|
|ColorSubSeq_4.txt|<code>426513685360047350000297200009359714A8241861000091000168151580002364300680003A96598A347843769857400A6400097AA7954800092474817831761497316490001524276A6500A5624634004387A00A43A8469000691315379452001000A31974157349A54983518931A8348A156A95613001413541A9439002154753A78200462600750062165A8001374793278000002A7732891489200000A217001100</code>|
|ColorSubSeq_5.txt|<code>002A7732891489200000A2170011005126487338623009009842900042A934A923754A00022551900006A001982380061270009A67218723A1004000745115590079219A45005003970000059A1388329A32A814700045996713A00995500821AA6620078166AA55A9128712981007622661177A145AA447744882277228800A12A00449944AA239A229933AA33980005A00000800813991188119922AA11A007007711673</code>|

Each subject then viewed these sequence in forward order, and then in a second scanning session in reverse order.

====Covariate design====
The analysis of the fMRI data was conducted within in a general linear model using covariates derived from the stimulus sequence.

<WRAP download round box 33%>**Sequence and covariates**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/coloradapt/ColorAdapt_DemoMatrices.mat]]\\ \\ Matlab ''.mat'' file containing the stimulus sequence and the covariates used in analysis.</WRAP>

The set of covariates included:

  * **Main effect**: A value of zero for every blank stimulus, and for every stimulus that follows a blank, and a value of unity for every other stimulus.
  * **New**: A value of zero for every blank and for every stimulus, except those stimuli that follow a blank, for which a value of unity is assigned.
  * **adapt_x^1**: The absolute value of the difference in hue number from the current stimulus to the prior stimulus, mean centered. A value of zero is assigned for stimuli that are blank or follow blank stimuli.
  * **adapt_x^2**, **adapt_x^3**, **adapt_x^4**: The higher polynomial versions of **adapt_x^1**, with each rendered orthogonal to the lower order polynomial elements.
  * **Categorical**: A value of one for every stimulus that has a hue distance from the prior stimulus of exactly 3 and crosses the categorical boundary, and a value of -1 for every transition of 3 that does not cross the boundary.
  * **direct_x^1**: The absolute value of the stimulus / hue #, mean centered. A value of zero is assigned for stimuli that are blank or follow blank stimuli.
  * **direct_x^2**, **direct_x^3**, **direct_x^4**: The higher polynomial versions of **direct_x^1**, with each rendered orthogonal to the lower order polynomial elements.
  * **Intercept**: a value of unity at every position.
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