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 år sedan
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BATCH_pRF_PadAndUpsample.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
BATCH_pRF_avg_BOLD_tseries.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
ReadMe.txt	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_AvgSessions.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_AvgSessions_even.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_AvgSessions_odd.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_PrepDatalist_M01.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_PrepDatalist_M02.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_avg_BOLD_tseries.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_prepCrossVal.m	4c6918ae5b gin commit from chris-mh16	3 år sedan
pRF_prepdata_avg.m	4c6918ae5b gin commit from chris-mh16	3 år sedan

		
			
			
				ReadMe.txt
			
		
		
	
			
		====================================
Workflow MRI pRF's
====================================

These pre-fitting scripts are located in the <..>/Analysis_code/MRI folder

1	pRF_prepdata_avg.m (batch: BATCH_pRF_PadAndUpsample.m)
	- Takes pRF_PrepDatalist_MONKEY.m as info on what preprocessed fMRI data to load
	- Creates timeseries of equal 230 volumes length by inserting NaNs
	- Saves as ses-XXXX-230vols.mat 
	- In <...>/Raw_data/MRI/Raw_matlab/us-padded//

2	pRF_avg_BOLD_tseries.m (batch: BATCH_pRF_avg_BOLD_tseries.m)
	- Takes the ses-XXXX-230vols.mat from <...>/Raw_data/MRI/Raw_matlab/us-padded//
	- Creates an average timecourse per session
	- Saves as medianBOLD_sess-xxxxxx.mat
	- In <...>/Raw_data/MRI/Raw_matlab/us-padded//

3	pRF_AvgSessions.m / pRF_AvgSessions_odd.m / pRF_AvgSessions_even.m
	- Takes the medianBOLD_sess-xxxxxx.mat from <...>/Raw_data/MRI/Raw_matlab/us-padded//
	- Averages across sessions
	- Saves as AllSessions-avg.mat / AllSessions-avg-odd.mat / AllSessions-avg-even.mat
	- Copies these files to <...>/Preprocessed_data/MRI//

4	pRF_prepCrossVal.m
	- Takes AllSessions-avg-odd.mat & AllSessions-avg-even.mat from <...>/Preprocessed_data/MRI//
	- Restructures
	- Saves as AllSessions-avg-cv.mat
	- In <...>/Preprocessed_data/MRI//

5	Copy <...>/Preprocessed_data/MRI//AllSessions-avg-cv.mat to LISA <...>/PRF/Data/MRI/cv//
	Run fits on LISA
	Copy fit results from LISA <...>/PRF/Results/ back to local <..>/FitResults/MRI//

6	Continue analysis in <..>/Analysis_code/PostFit
		
		

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