[[FrontPage]]
#contents
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'''~
&color(red){CAUTION!! :Keep the raw data separate so that you have a backup};
*EPI data processing [#e9ea3183]
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]]''
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'''~
&color(red){CAUTION!! :If the data was taken using shot interleaved sequence (intlv="y"), you should skip ssc process.};
&color(red){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 [#e28182ba]
[[pp for Monkey 3Danat>pp for 3D anatomy]]
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]&br;
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 [#y19854eb]
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'''