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Data processing

!!Under construction!!

Suppose you have the data below.

EPI data: exp_date/raw/run.fid

noise data: exp_date/raw/noise.fid

epibsi run.fid
epibsi noise.fid

(!)epibsi overwrites your original data. You must copy the original data and apply 'epibsi' onto the copied data.

Make a symbolic link of .car file to run.fid directory

cd run.fid/
ln -s ../../physio/date_01.car ./

Peak

peak

→ acq.peak.bit, cardio.peak.bit, respir.peak.bit

Physiological noise correction

pp -physiofix -outtype 1 run.fid run.phys.edt
pp -outtype 1 noise.fid noise.edt

→ run.phys.edt/epr

Making mask
mask data needs to be in float type sdt/spr files.
Data part:fixed value(e.g.1), Non-data part:0

By using view3d
pp run.fid run.sdt
merge_coils run
rmvol run-pw
sdtstat run-pw -ave
smooth2d run-pw-ave 0.2 (Other option:smooth3d)
view3d run-pw-ave-sm2.sdt run-pw-ave.sdt 
Then create run-pw-ave-sm2Msk.sdt
sdtmv run-pw-ave-sm2Msk mask

Making mask data on view3d

By using Stimulate
pp run.fid run.sdt
merge_coils run
Load the run-pw.sdt/spr and make mask.sdt/spr as float.

tSENSE recon

tsense_test -full run.phys -remove -recon run.phys.tsns -mask mask -noise noise

Oscillation removal

tsns_pp2 run.phys.tsns