ChrisKlink/NHP-pRF: Population receptive fields in non-human primates from whole-brain fMRI and large-scale neurophysiology in visual cortex.

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Chris Klink 4c6918ae5b gin commit from chris-mh16		3 vuotta sitten
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ExampleElectrode.mat	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ExampleVoxel.mat	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ReadMe.txt	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_2dPRF_ephys.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_BasicProc_AllFits_cv1.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_Batch_Combine_MRI_SliceChunks.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_CollectAllFittingResults.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_Combine_MRI_SliceChunks_cv.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_ExampleElectrode.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_ExampleVoxel.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_GetAtlasTable.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_GetEphys_pRF.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_GetMRI_pRF.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_GetROIidx.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_StatsAndPlots.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_xmod_stats.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten
ck_xmod_stats_lowfreqlfp.m	4c6918ae5b gin commit from chris-mh16	3 vuotta sitten

		
			
			
				ReadMe.txt
			
		
		
	
			
		====================================
Workflow POSTFIT pRF's (matlab)
====================================

These post-fitting scripts are located in the <..>/prfCode/PostFit/matlab folder

1	ck_Batch_Combine_MRI_SliceChunks.m
	- Uses ck_Combine_MRI_SliceChunks.m to put chunks back together
	- Takes slice chunks from <..>/FitResults/MRI//
	- Combine them
	- Save volumes in same folder

2	ck_CollectAllFittingResults.m
	- ck_GetMRI_pRF.m
		- combines results from 2 animals
		- Gets data from <..>/FitResults/MRI/ saves data in <..>/FitResults/MRI/Combined
		- Adds D99 atlasses
			- ck_GetAtlasTable.m gets the atlas info
	- ck_GetEphys_pRF.m
		- combines results from 2 animals
		- Gets and saves data in <..>/FitResults/EPHYS
 	- Combines MRI and Ephys
 	- Saves as AllFits.cv1.mat in <..>/FitResults/MULTIMODAL

3	Run ck_BasicProc_AllFits_cv1.m
	- Takes data from <..>/FitResults/MultiModal	
	- Re-structures
	- Saves back as tables and structures in <..>/FitResults/MultiModal
		
4	ck_StatsAndPlots.m
	- Long script that creates plots and runs statistics etc
	- Uses: 
		- ck_GetROIidx.m
			- get an ROI index back when querying with label
		- ck_xmod_stats.m 
			- Runs the LMM for crossmodal statistics
        - ck_xmod_stats_lowfreqlfp.m 
			- Runs the LMM for crossmodal statistics for pos/neg low freq lfp
    - Contains comments on where manuscript figures are generated





======================================
Example pRF-fit electrode/voxel
# Basis of Figure 1E 
======================================

1	ck_ExampleVoxel.m
    - for MRI 

2	ck_ExampleElectrode.m
    - for EPHYS

		
		

datacite.yml
Title	Population receptive fields in non-human primates from whole-brain fMRI and large-scale neurophysiology in visual cortex.
Authors	Klink,Chris;Netherlands Institute for Neuroscience;ORCID:0000-0002-6784-7842 Chen,Xing;Netherlands Institute for Neuroscience Vanduffel,Wim;KU Leuven;ORCID:0000-0002-9399-343X Roelfsema,Pieter;Netherlands Institute for Neuroscience;ORCID:0000-0002-1625-0034
Description	This data-set contains all data and code for the paper 'Population receptive fields in non-human primates from whole-brain fMRI and large-scale neurophysiology in visual cortex.'
License	Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References	P.C. Klink, X. Chen, W. Vanduffel, & P.R. Roelfsema (2021). Population receptive fields in non-human primates from whole-brain fMRI and large-scale neurophysiology in visual cortex. eLife [doi:10.7554/eLife.67304] (IsSupplementTo)
Funding	NWO, Crossover Program 17619 'INTENSE' NWO, STW-Perspectief P15-42 'NESTOR' NWO, VENI 451.13.023 EU FP7, ERC-339490 'Cortic_al_gorithms' EU, Human Brain Project (agreements 720270 and 748 785907, SGA1 and SGA2) Friends Foundation of the Netherlands Institute for Neuroscience
Keywords	Neuroscience Neuroimaging Neurophysiology Non-human primate Population receptive field
Resource Type	Dataset