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  • 5 (2007-02-14 (Wed) 00:25:33)
  • 6 (2012-04-01 (Sun) 20:23:09)

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Postprocessing†

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&#12288;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>

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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)

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†

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†

STIMULATE

mask file: mask.sdt
mask run1_SCSA_3DMCTSf mask<RET>

Temporal filtering†

bp_filt run1_SCSA_3DMCTSfM.sdt -h 5<RET>