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  • 1 (2012-12-19 (Wed) 19:08:26)
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  • 3 (2012-12-24 (Mon) 17:23:35)
  • 4 (2013-02-04 (Mon) 23:22:53)
  • 5 (2013-02-13 (Wed) 18:18:13)
  • 6 (2013-02-13 (Wed) 22:15:39)
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  • 8 (2015-07-28 (Tue) 01:49:23)
  • 9 (2015-09-03 (Thu) 21:24:30)

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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

peak

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

Physiological noise correction

pp -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

Motion correction
To apply motion correction to run.phys-pw.sdt data using 1st volume as a target,

mcafni run.phys-pw

※You can change the target volume by adding file name and the volume number (default=1th volume).
e.g.) target volume = 20th volume of target.sdt file

mcafni run.phys-pw target 20  

→ run.phys-pw-aMC.sdt/spr

Slice scan time correction

mkslc run.fid > run.fid/slice.txt
ssc run.phys-pw-aMC run.fid/slice.txt

→ run.phys-pw-aMC.SC.sdt/spr

High pass filter

bp_filt run.phys-pw-aMC.SC -h 5(*)

*It depends on your task design

→ run.phys-pw-aMC.SC.HP.sdt/spr

sdt4to2 run.phys-pw-aMC.SC.HP
sdt2spm run.phys-pw-aMC.SC.HP
*sdt4to2 is for BV(float>short conversion)

→run.phys-pw-aMC.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]
This procedure may not be necessary for the later processing. It depends on your application for the farther processing.

resize3d 3d_anat-pw 256

sdt2spm 3d_anat-pw (+/-)
+: NIFTI(.nii) output
-: ANALYZE(.hdr/img) output

→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 1 -2 3 4) *if necessary
sdt4to2 2d_anat-pw(X)
sdt2spm 2d_anat-pw(X)
*sdt4to2 is for BV(float>short conversion)

→2d_anat-pw(X)_analyze/.hdr/img