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FolderStructure

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

Individual data processing†

>cd 0001<RET>
>dcms2sdt . <RET> : dicom to sdt data conversion(unifying the multiple dicom files)
(>demosaic all<RET> : decompose the mosaic format (EPI/DTI data))
>sdt2to4 all<RET> : 2-byte unsigned short to 4-byte float data conversion

Now we are updating the dcms2sdt command to pack the 3 procedures above. The new command is available as "dcms2sdt_new".

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

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 all_dM.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

despike_tst all_dM<RET> Remove the slow drift and sharp spikes
physiofix all_dMDs acq.peak.new.bit resp.peak.bit card.peak.bit<RET> Retrospective physiological noise removal
mcafni all_dMDs<RET> Motion correction by afni. mc2dafni is also available for 2d motion correction.
ssc2 all_dMDs<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.