History of DataProcessing3T (No. 12)
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- 1 (2016-06-23 (Thu) 01:20:33)
- 2 (2016-07-01 (Fri) 03:58:22)
- 3 (2016-07-12 (Tue) 02:42:52)
- 4 (2016-08-08 (Mon) 04:28:28)
- 5 (2016-08-09 (Tue) 02:12:03)
- 6 (2016-09-02 (Fri) 08:29:49)
- 7 (2017-03-15 (Wed) 07:15:27)
- 8 (2017-03-16 (Thu) 02:56:45)
- 9 (2017-04-04 (Tue) 02:35:57)
- 10 (2017-05-12 (Fri) 11:58:59)
- 11 (2017-06-02 (Fri) 08:28:17)
- 12 (2017-06-23 (Fri) 06:53:21)
- 13 (2017-07-10 (Mon) 01:03:51)
- 14 (2017-12-18 (Mon) 06:47:48)
- 15 (2017-12-19 (Tue) 03:09:42)
- 16 (2019-02-27 (Wed) 16:04:53)
- 17 (2019-08-18 (Sun) 17:52:25)
- 18 (2020-03-18 (Wed) 15:54:30)
- 19 (2020-12-23 (Wed) 22:50:13)
- 20 (2020-12-24 (Thu) 19:20:46)
###--- 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†
0051:1016 | 0051:1019 | ||
Abbreviation | Image Type | Abbreviation | Image Type |
ADC | Apparent Diffusion Coefficient Map | A(y) | Number of averages |
ADD | Image resulting from an addition | FS | fat saturation |
AVERAGE | VRT image | WS | Water saturation |
BLACK IMAGE | Graphic image or Grahpics and table image | WE | Water excitation |
SAT (y) | Number of saturation regions | ||
DB | Dark blood | ||
IR | Inversion recovery | ||
SR | Saturation recovery | ||
G(x) | Grid tag with x mm grid distance | ||
L (x) | Line tag with x mm line distance | ||
MT | MTC pulse | ||
PFP | Partial Fourier for Phase(it's PPF in the manual) |