Postprocessing
Last-modified: 2015-07-28 (Tue) 10:49:23 (3208d)
Postprocessing †
hana: MacProMid2010 2.66GHzXenonx2(12Core)32GB Memory
256x256x180x16(3D data) fid2sdt:135sec(hana) merge_coils:8sec(hana)
3D anatomical data †
High resolution sagittal base 3D data(creating v16 data) †
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 †
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 †
EPI data correction(Reference scan & Navigator echo)
cd ../epirri<RET> epirri4b run1.fid<RET> *Be careful the data is overwritten.
Peak †
peak<RET> load *.car data and make 3 files(acq.peak.bit cardio.peak.bit respir.peak.bit)
Physiofix †
postproc -dc -physiofix run1.fid run1.pp1.sdt<RET> DC artifact removal & physiofix
First volume(reference) removal †
rmvol run1.pp1<RET>
Convert data type into short integer †
sdt4to2 run1.pp1<RET>
Convert to Analyze format(for BrainVoyager) †
sdt2spm run1.pp1<RET>
BrainVoyager †
Load analyze format data Preprocessing fmr data -slice scan time correction -3D motion correction
Make output as Analyze format (run1_SCSA_3DMCTS_0*.img)
†
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 †
mask file: mask.sdt mask run1_SCSA_3DMCTSf mask<RET>
Temporal filtering †
bp_filt run1_SCSA_3DMCTSfM.sdt -h 5<RET>