NHP-pRF/Analysis_code/MRI/ReadMe.txt

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Workflow MRI pRF's
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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/<subject>/

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/<subject>/
	- Creates an average timecourse per session
	- Saves as medianBOLD_sess-xxxxxx.mat
	- In <...>/Raw_data/MRI/Raw_matlab/us-padded/<subject>/

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/<subject>/
	- Averages across sessions
	- Saves as AllSessions-avg.mat / AllSessions-avg-odd.mat / AllSessions-avg-even.mat
	- Copies these files to <...>/Preprocessed_data/MRI/<subject>/

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

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

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