# mriSinaiAnalysis
Analysis code for the paper:
CP Gentile, M Spitchan, HO Taskin, A Bock, GK Aguirre. (in revision) Temporal sensitivity for achromatic and chromatic flicker across the visual cortex. J Neuroscience.
Overview of analysis pipeline
Raw fMRI data were stored on Flywheel
Pre-processing using fmriprep and ICA aroma pursued using Flywheel gears
The time-series data were analyzed using forwardModel. To do so, the non-linear fitting routine requires a "stimulus" matrix, and details regarding the order and timing of the stimulus events. These elements were created using the functions:
- makeStimStruct (downloads the raw "results" files and subject responses created by the computer that presented the stimuli at the time of scanning)
- loadStimStructCellArray (loads the "stimStruct" that summarizes these raw files)
- getAttentionEvents (finds where in the stimStruct attention events took place)
- stimConstructor_gka_asb (assembles the "stimulus" matrix from the "stimStruct")
- stimConstructor_cgp (subject cgp was studied with a different stimulus generation system; the stimulus matrix for this subject was generated in one step from the raw, "results" files generated by the stimulus presentation computer at the time of scanning).
The result of this stage of analysis were "stimulus.mat" files that were uploaded to Flywheel and used as inputs, along with the pre-processed fMRI data, to the forwardModel. The forwardModel gear runs on Flywheel were defined using the CSV files located within the "submitGears" directory.
The output of the forwardModel were the files "HEROxxx1_mtSinai_results.mat", where xxx is the subject ID. These files are stored in the data directory of this repo. The "mtSinai_results" files contains, for each grayordinate in the HCP CIFTI space, the parameters of the fit of the forwardModel. These parameters are effectively a beta weight for the amplitude of response to each trial type from each acquisition, with an additional parameter for the response to the attention event in each acquisition, and three parameters for the shape of the HRF found to best fit the responses for that grayordinate. The results file also contains an R2 value of the model fit to the time-series data for that coordinate, excluding the effect of the attention events.
These model parameters then served as inputs to subsequent analyses. The primary analysis was then pursued using the routine:
- fitWatsonModelVertex
located in the "temporalModel" directory. This function fits the Watson double-exponential TTF to the response parameters at each vertex. The result of this fitting operation was stored in the data results directory for each subject with the name "HEROxxx1_WatsonFit_results.mat".
The figures for the paper were then generated using the routines located in the figures directory. These figures make use of the mtSinai and Watson fit results, as well as retinotopic regions of interest defined using cortical topology (these retino files and regions of interest masks are stored in the data directory).
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接收后方向受阻和闪烁频率刺激的7T数据分析matlab代码.zip
共102个文件
m:62个
nii:14个
mat:12个
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接收后方向受阻和闪烁频率刺激的7T数据分析matlab代码.zip (102个子文件)
cumsumall.cpp 5KB
mtSinai_forwardModel_avgV1_attentionControl.csv 42KB
mtSinai_forwardModel_LGN_mtSinai.csv 31KB
mtSinai_forwardModel_ExtendedMask_mtSinai.csv 31KB
mtSinai_forwardModel_avgV1_mtSinai.csv 30KB
Patterson_2024_JNeurosci.json 1KB
plasmaColorMap.m 15KB
mtSinaiAdapt.m 12KB
Fig3_lgnAndV1.m 12KB
combinator.m 12KB
fitCSTModelBootstrap.m 11KB
stimConstructor_gka_asb.m 10KB
createFieldMap.m 9KB
stimConstructorAttenControl_gka_asb.m 9KB
splatterCalcs.m 9KB
Fig9_fitsByVertexWithRGCModel.m 8KB
Fig4b_v1AcrossEcc_withWatsonFit.m 7KB
FigSx_decodeTemporalFreq.m 7KB
Fig5b_freqByVisualArea.m 7KB
Fig4a_v1FitsByVertex.m 6KB
watsonTemporalModel.m 6KB
FigSx_attentionControl.m 6KB
splatterCalcsTable.m 6KB
deriveFisherInfo.m 5KB
makeStimStruct.m 5KB
loadMRIResponseData.m 5KB
Fig5a_peakFreqMaps.m 5KB
fitWatsonModelVertex.m 4KB
stimConstructorAttenControl_cgp.m 4KB
FigSx_visualFieldTempSens.m 4KB
plot.m 4KB
stimConstructor_cgp.m 4KB
FigSx_attentionResponseMaps.m 4KB
Fig1c_modulationSPDs.m 3KB
loadStimStructCellArray.m 3KB
figuresize.m 3KB
Patterson_2024_JNeurosciLocalHookTemplate.m 3KB
FigX_adaptWithinTrial.m 3KB
update.m 3KB
modelAdaptation.m 3KB
FigSx_hrfDelayMaps.m 3KB
Fig2b_averageTimeSeries.m 2KB
setbounds.m 2KB
neuralForward.m 2KB
freqDetectFromLit.m 2KB
genprojection.m 2KB
fitWatsonModel.m 2KB
FigSx_carryOverEffects.m 2KB
metric.m 2KB
nonlcon.m 2KB
Fig2a_averageR2Maps.m 1KB
forward.m 1KB
getAttentionPerformance.m 1KB
results.m 1KB
prep.m 1KB
returnCSTFitAcrossEccen.m 1KB
initial.m 1KB
simpleFFT.m 982B
seeds.m 947B
getAttentionEvents.m 892B
objective.m 879B
simpleIFFT.m 833B
ciftiMakePseudoHemi.m 661B
clean.m 620B
genflobsbasis.m 572B
cumsumall.m 494B
escapeFileCharacters.m 214B
tbLocateProjectSilent.m 203B
HEROasb1_mtSinai_results.mat 47.61MB
HEROasb1_WatsonFit_results.mat 6.16MB
HEROcgp1_WatsonFit_results.mat 5.16MB
Cache-LMinusMDirectedXEccentricity-BoxCRandomizedLongCableCStubby1NoLens_ND10_ContactLens_0_5mm-SpotCheck.mat 4.59MB
Cache-SDirectedXEccentricity-BoxCRandomizedLongCableCStubby1NoLens_ND10_ContactLens_0_5mm-SpotCheck.mat 4.58MB
Cache-LightFluxXEccentricity-BoxCRandomizedLongCableCStubby1NoLens_ND10_ContactLens_0_5mm-SpotCheck.mat 4.57MB
HEROcgp1_avgV1_attentionControl_results.mat 2.63MB
HEROasb1_avgV1_attentionControl_results.mat 2.6MB
HEROcgp1_avgV1_mtSinai_results.mat 1.64MB
HEROasb1_avgV1_mtSinai_results.mat 1.62MB
HEROcgp1_LGN_mtSinai_results.mat 1.51MB
HEROasb1_LGN_mtSinai_results.mat 1.48MB
README.md 3KB
README.md 2KB
README.md 18B
cumsumall.mexw32 48KB
HEROasb1_angle.dscalar.nii 974KB
HEROasb1_sigma.dscalar.nii 974KB
HEROcgp1_angle.dscalar.nii 974KB
HEROcgp1_eccen.dscalar.nii 974KB
HEROasb1_eccen.dscalar.nii 974KB
HEROcgp1_lgn.dtseries.nii 973KB
HEROasb1_lgn.dtseries.nii 973KB
HEROcgp1_benson.dscalar.nii 972KB
HEROasb1_benson.dscalar.nii 972KB
HEROasb1_wang.dscalar.nii 972KB
HEROasb1_curvature.32k_fs_LR.dscalar.nii 569KB
HEROcgp1_curvature.32k_fs_LR.dscalar.nii 569KB
HEROasb1_curvature_binary.32k_fs_LR.dscalar.nii 568KB
HEROcgp1_curvature_binary.32k_fs_LR.dscalar.nii 568KB
splatter_LMinusM.pdf 84KB
splatter_S.pdf 64KB
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