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FolderStructure

###--- Under construction ---###

Individual data processing†

>dcms2sdt 0007 <RET> : dicom to sdt data conversion(unifying the multiple dicom files and doing demosaic)
The data type of output sdt/spr files is float.

If you want to transfer the data to the other software,
>sdt2spm m0007 + <RET>
Then NIFTI-1 format file is ready as all.nii

All data processing†

>dcmall <RET>
Process all of the folders(00??) and make sdt/spr files.

EPI data(fMRI data)†

Making peak.bit files

car_anlz 170101-01.car 01<RET>
Now you get 01.acq.bit, 01.cardio.bit and 01.respir.bit.
(You can still use the old 'peak' command to make the bit files)

Edit the acq.peak.bit file

start from m0007.sdt/spr and peak.bit files
You need to correct the acq.peak.bit file.
>acqbitc acq.peak.bit acq.peak.new.bit 37<RET>
The number, N=37,  need to be adjusted to fit to your data. The acquisition pulses were recorded for individual volumes but we need to have same number of triggers as the number of acquisition(e.g. number of slices(or slice sets for MB) x number of volumes). It must be equal to the number of timing recorded as mosaic_timmng. We'll put the number of additional triggers, so in N=37 case,38 triggers were prepared for each volumes after the acqbitc processing.

Main postprocessing

mcafni m0007<RET> Motion correction by afni. mc2dafni is also available for 2d motion correction.
glmdenoise m0007-aMC +<RET> Remove the spike or the step noise caused by subject's motion
despike m0007-aMC_gdn<RET> Remove the slow drift and sharp spikes
physiofix m0007-aMC_gdnDs acq.peak.new.bit resp.peak.bit card.peak.bit<RET> Retrospective physiological noise removal
ssc2 m0007-aMC_gdnDs-pp<RET> Slice scan time correction
...
(sdtt, sdtcc, sdtglm,...)

DTI data†

To make gradient table file,
>dcms2gtb<RET>
Then grd.txt has gradient(x,y,z)  and b-value
You can use this for Diffusion Toolkit(Trackvis).
This procedure is likely unnecessary because Diffusion Toolkit has standard Siemens gradient setting as defaults.

DICOM parameter meanings†