*Postprocessing [#q63c8f29]
hana: MacProMid2010 2.66GHzXenonx2(12Core)32GB Memory~
256x256x180x16(3D data)
fid2sdt:135sec(hana)
merge_coils:8sec(hana)
*3D anatomical data [#r17f67ad]
**High resolution sagittal base 3D data(creating v16 data) [#z48ef00a]
For mprage01.fid
$> fid2sdt mprage01 - <RET> (1*)
$> merge_coils mprage01 <RET>
$> pp3d mprage01-pw <RET> (2*)
$> vmark mprage01-pw-dT 5<RET> (3*)
$> raxis mprage01-pw-dT-MK5 2 1 -3 4 <RET> (4*)
$> resize3d mprage01-pw-dT-MK5X <RET>
$> sdt4to2 mprage01-pw-dT-MK5X <RET>
$> sdt2v16 mprage01-pw-dT-MK5X <RET>
Now we have mprage01-pw-dT-MK5X.v16
1*) '-' is for degibbs algorithm application(Gibbs ringing artifact removal).
2*) If you don't have good data after this, you should try this command with non-default parameters.
Or you may want to finalize your data with "pp3d mprage01-pw 15 1 0 90".
3*) If you don't need to have the left side marker, you can skip this.
4*) If you find Left-Right reverse in BrainVoyager, you should put 3 instead of -3 here.
*OLD description [#q4f15f42]
This is one example of EPI data processing.~
BrainVoyager is used for 3D motion correction.~
[Example]
raw/run1.raw.fid (original data)
cp -r run1.raw.fid ../epirri/run1.fid<RET>
cd ../epirri<RET>
ln -s ../physio/070101-01.car run1.fid/<RET>
**EPIRRI [#reb787dd]
EPI data correction(Reference scan & Navigator echo)
cd ../epirri<RET>
epirri4b run1.fid<RET>
*Be careful the data is overwritten.
**Peak [#x425542a]
peak<RET>
load *.car data and make 3 files(acq.peak.bit cardio.peak.bit　respir.peak.bit)
**Physiofix [#o8e85155]
postproc -dc -physiofix run1.fid run1.pp1.sdt<RET>
DC artifact removal & physiofix
**First volume(reference) removal [#i1727daa]
rmvol run1.pp1<RET>
**Convert data type into short integer [#edb8962f]
sdt4to2 run1.pp1<RET>
**Convert to Analyze format(for BrainVoyager) [#f5b55d79]
sdt2spm run1.pp1<RET>
-------------------------------------------
**BrainVoyager [#ab6e8072]
Load analyze format data
Preprocessing fmr data
-slice scan time correction
-3D motion correction
Make output as Analyze format
(run1_SCSA_3DMCTS_0*.img)
-------------------------------------------
** [#u8963dbd]
cat run1_SCSA_3DMCTS_0*.img > run1_SCSA_3DMCTS.sdt<RET>
endianflip run1_SCSA_3DMCTS.sdt run1_SCSA_3DMCTSf.sdt s<RET>
cp run1.pp1.spr run1_SCSA_3DMCTSf.spr<RET>
** Make a mask file and apply it [#p66f0f7d]
[[STIMULATE]]
mask file: mask.sdt
mask run1_SCSA_3DMCTSf mask<RET>
** Temporal filtering [#r24e7670]
bp_filt run1_SCSA_3DMCTSfM.sdt -h 5<RET>