Data processing
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 †
For tSENSE data processing, go to TsenseDataProcessing For SENSE data processing, go to SenseDataProcessing
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
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
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
CAUTION!! :If the data was taken using shot interleaved sequence (intlv="y"), you should skip ssc process.[ShotInterleave]
3D Motion correction
Appling motion correction to run.phys-pw.sdt using 1st volume of this data as a target
(※If the data set contains only a few slices, you can use mc2dafni for 2D motion correction)
mcafni run.phys-pw.SC mc2dafni run.phys-pw.SC
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.SC target 20
→ run.phys-pw.SC-aMC.sdt/spr
High pass filter
bp_filt run.phys-pw.SC-aMC -h 5(*)
*It depends on your task design
→ run.phys-pw.SC-aMC.HP.sdt/spr
sdt4to2 run.phys-pw.SC-aMC.HP sdt2spm run.phys-pw.SC-aMC.HP *sdt4to2 is for BV(float>short conversion)
→run.phys-pw.SC-aMC.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