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QunjunLIANG/Pick Up Sam Analysis Scripts

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README
MulanPSL-2.0

Materials of Pick Up Sam

For opening the necessary scripts we used in Pick Up Sam. Here, we are grateful for the supports given by Bradley Buchsbaum in RSA.

Introduction of Document Tree

Behavioral_analysis

/raw_data contains the data recorded by our experimental program coding with C# on the platform of Unity3D .

Behavioral_analysis_pipeline.R is the R script used to perform linear mixed-effect model (LMM) and generate the Fig. 4 in our paper.

The parameteric estimation of the LMM was performed with lmerTest and the simple effect in ANOVA was given by sjstats.

The visualization of LMM results was based on ggplot2 and its extended packages, including ggsignif, ggstatsplot and ggeasy.

GLM1_related

/GLM1_related contains the design and results of the general linear model 1 in our paper.

The GLM1 was conducted using FSL's Feat. GLM1_design.fsf is the design file using to run Feat in first-level analysis, and the GLM1_design_matrix.png is the visual check f design matrix in GLM1_design.fsf.

GLM1_run_bash.sh is the script to run fist-level GLM1 for batch process.

The NIfTI files in this directory are the z-value map of the modulation effect separated by conditions. The p-value of these maps are already corrected by a cluster probability threshol from GRF-theory.

GLM2_related

Files in /GLM2_related are similar to that in /GLM1_related, please check the upper section to identify the files in this directory.

RSA_related

/RSA_related contains the R script to run whole-brain searchlight for RSA, and the post-stat to fisher-z transform and smoothing the searchlight results.

step_3_run_randomize.sh is the bash script to call FSL's randomise for group-level one-sample t-test.

Updated at 2022/03/02

The superaddition of ROI analysis in GLM and RSA

GLM_ROI_analysis contains the ROI-based analysis in group-level inference of the activation in the PHC.

RSA_ROI_analysis contains the ROI-based analysis in RSA.

The application and C script of "Pick Up Sam"

The .zip package named PickUpSam_Unity.zip contains everything you need to run "Pick Up Sam" on your computer. It is worth to note that the application was only tested on Windows 10.

PickUpSam_programming documented the core C-sharp scripts in "Pick Up Sam" programming. The script named loopControl.cs controled the condition arrangement and testing distance assignment during the task. CoreControl.cs was response to the process control within a single trial, like the object placement, target vanishing, car stop, etc.

Updated at 2022/03/16

Replace the modulation effect of each condition with the contrast of SL-LF and AL-LF

GLM1 contrast results: /GLM1_related/ClusterReport_SL-LF_contrast.html and /GLM1_related/Result_SL-LF_contrast_thresh_zstat.nii.gz

GLM2 contrast results: /GLM2_related/ClusterReport_SL-LF_contrast.html and /GLM2_related/Result_SL-LF_contrast_thresh_zstat.nii.gz

Copyright (c) [Year] [name of copyright holder] [Software Name] is licensed under Mulan PSL v2. You can use this software according to the terms and conditions of the Mulan PSL v2. You may obtain a copy of Mulan PSL v2 at: http://license.coscl.org.cn/MulanPSL2 THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE. See the Mulan PSL v2 for more details. Mulan Permissive Software License,Version 2 Mulan Permissive Software License,Version 2 (Mulan PSL v2) January 2020 http://license.coscl.org.cn/MulanPSL2 Your reproduction, use, modification and distribution of the Software shall be subject to Mulan PSL v2 (this License) with the following terms and conditions: 0. Definition Software means the program and related documents which are licensed under this License and comprise all Contribution(s). 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You may obtain a copy of Mulan PSL v2 at: http://license.coscl.org.cn/MulanPSL2 THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE. See the Mulan PSL v2 for more details.

简介

This repo contains the scripts used in analyzing the data of Pick Up Sam. 展开 收起
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MulanPSL-2.0
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Pick Up Sam Analysis Scripts
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