Backup of Data processing (No. 2)
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Suppose you have the data below.
EPI data: exp_date/raw/run.fid
Physiological data: exp_date/physio/date_01.car
2D anatomical data: exp_date/raw/2d_anat.fid
3D anatomical data: exp_date/raw/3d_anat.fid
CAUTION!! :Keep the raw data separate so that you have a backup
EPI data processing †
epibsi run.fid
Make a symbolic link of .car file to run.fid directory
cd run.fid/ ln -s ../../physio/date_01.car ./
peak
→ acq.peak.bit, cardio.peak.bit, respir.peak.bit
Physiological noise correction
pp38 -physiofix run.fid run.phys.sdt
→ run.phys.sdt/spr
Merge data from different coils
merge_coils run.phys
→ run.phys-pw.sdt/spr
Remove reference volume
rmvol run.phys-pw
Slice scan time correction
mkslc run.fid > run.fid/slice.txt ssc run.phys-pw run.fid/slice.txt
→ run.phys-pw.SC.sdt/spr
High pass filter
bp_filt run.phys-pw.SC -h 5(*)
*It depends on your task design
→ run.phys-pw.SC.HP.sdt/spr
sdt4to2 run.phys-pw.SC.HP sdt2spm run.phys-pw.SC.HP
→run.phys-pw.SC.HP_analyze/.hdr/img
3D anatomical data processing †
fid2sdt 3d_anat.fid
→3d_anat.sdt/spr
merge_coils 3d_anat
→3d_anat-pw.sdt/spr
※for 3D high anatomical data [256,256,180] -> [256,256,256]
resize3d 3d_anat-pw 256
sdt2spm 3d_anat-pw +
→3d_anat-pw_analyze/.hdr/img/.nii
2D anatomical data processing †
fid2sdt 2d_anat.fid
→2d_anat.sdt/spr
merge_coils 2d_anat
→ 2d_anat-pw.sdt/spr
raxis 2d_anat-pw 2 1 3 4 (if necessary) sdt4to2 2d_anat-pw(X) sdt2spm 2d_anat-pw(X)
→2d_anat-pw(X)_analyze/.hdr/img