[[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
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''
tsnspp2 run.phys.tsns
tsns_pp2 run.phys.tsns