NHP-pRF/Analysis_code/MRI

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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//

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