Extraction of Slice Ordering in DICOM Image
Download Complete Package in Zip File
Slice ordering (SO) is set in a protocol for MR scan and the information is saved in DICOM image header. For example, Sagittal (R)ight >> (L)eft, Coronal (A)nterior >> (P)osterior, Transverse (F)oot >> (H)ead. The released software, checkslice reads the slice order direction from a DICOM file, and the MATLAB script provides an idea of how to check SO from EPI data of multiple projects and studies. The releases were tested with CentOS and Ubuntu. If a bug is found, please report to Dr. Moon, moonc@upmc.edu.
Download “Release.zip” and unzip it on your computer disc. The unzipped folders and files are,
PhantData/
BOLDSLICEORDER_mMR/ (the sequence name includes transverse SO, ex, HF. If none, it is FH)
BOLDSLICEORDER_Prisma1/ (the sequence name includes transverse SO, ex, FH or HF)
checkslice.m
…
checkslice (under different Linux OS)
1. checkslice binary
Description: Ubuntu 16.04.7 LTS
Release: 16.04
Codename: xenial
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic
centos-release-8.2-2.2004.0.1.el8.x86_64
Requirement of additional software: None
The path of checkslice should be visible to a user, for example, /usr/local/bin/checkslice
- Download the binary file checkslice
- Type checkslice in command line for help
This program extract Slice ordering from DICOM file!
Usage : checkslice -i dicom.ima -sd [0/1/2] -so [0/1] @chm, 02/18/2021
-i dicom.ima: Siemens DICOM file
-sd [0/1/2]: Slice direction 0-sag, 1-cor, 2-tra, other – all(default)
-so [0/1]: Slice ordering (MB=1) 1-yes print, 0-no print(default)
- Type checkslice -i dicomfile …
Examples,
checkslice -i BOLDSLICEORDER.IMA
Slice Sagittal direction is R >> L (if image slice is sagittal)
Slice Coronal direction is A >> P (if image slice is coronal)
Slice Transverse direction is H >> F (if image slice is transverse)
checkslice -i BOLDSLICEORDER.IMA -sd 2
H >> F
checkslice -i BOLDSLICEORDER.IMA -sd 3 -so 1
Slice Sagittal direction is R >> L
Slice Coronal direction is A >> P
Slice Transverse direction is H >> F
Slice ordering is INTERLEAVED 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44
2. MATLAB script, checkslice.m
% MATLAB script to read Slice ordering in EPI DICOM image
%
% 02/26/2021, Chan Hong Moon, PhD
%
% Add path for necessary m codes
addpath('/your_matlab_script_folder_path/PhantData');
% Set your study folder path for EPI DICOM
pfolderlist = {...
'/your_study_folder_path/PhantData/BOLDSLICEORDER_mMR'...
'/your_study_folder_path/PhantData/BOLDSLICEORDER_Prisma1'...
};
npfolderlist = length(pfolderlist);
% Sequence naming
EPInamelist = {...
'*EP2D_*'...
'*BOLD*'...
};
nepilist = length(EPInamelist);
% Loop for slice ordering
lcount = 1;
for ll=1:npfolderlist
pfolder = pfolderlist{1,ll};
fprintf(2,'%s\n', pfolder);
Pfolder = [pfolder '/'];
icheck = 0;
for i=1:nepilist
if icheck>=1
break;
end
episeqname = EPInamelist{1,i};
direpiBOLD = dir([Pfolder episeqname]);
lcount = 1;
nepiBOLD = length(direpiBOLD);
for k=1:nepiBOLD,
epiBOLD = direpiBOLD(k,1).name;
P = [pfolder '/' epiBOLD '/'];
dirdicom = dir([P '*.IMA']);
if (isempty(dirdicom))
dirdicom = dir([P 'MR.*']);
end
nfiles = length(dirdicom);
% read DICOM header including CSA information
[dcminfo, err] = dicm_hdr([dirdicom(1).folder '/' dirdicom(1).name]);
% checkslice in terminal
dicomfilename = [dirdicom(1).folder '/' dirdicom(1).name];
strcmd = ['checkslice -i ' dicomfilename ' -sd 2'];
[s,w] = unix(strcmd);
I = find(w~=' ');
w = w(I); w=w(1:end-1);
% report
disp([num2str(lcount) ': ' epiBOLD ': ' w(1:end)]);
lcount = lcount + 1;
icheck = 1;
end
end
end
% rm path for necessary m codes
rmpath('/ your_matlab_script_folder_path/PhantData');
Outputs are like as follows,
>> checkslice
/your_study_folder_path/PhantData/BOLDSLICEORDER_mMR
1: EP2D_BOLD_MB1_SLC45_0002: F>>H
2: EP2D_BOLD_MB1_SLC45_ASC_0015: F>>H
3: EP2D_BOLD_MB1_SLC45_DSC_0016: F>>H
4: EP2D_BOLD_MB1_SLC46_0003: F>>H
5: EP2D_BOLD_MB1_SLC46_HF_0004: H>>F
6: EP2D_BOLD_MB2_SLC46_0008: F>>H
7: EP2D_BOLD_MB2_SLC46_SBREF_0007: F>>H
8: EP2D_BOLD_MB3_SLC45_0006: F>>H
9: EP2D_BOLD_MB3_SLC45_SBREF_0005: F>>H
10: EP2D_BOLD_MB3_SLC48_0012: F>>H
11: EP2D_BOLD_MB3_SLC48_HF_0014: H>>F
12: EP2D_BOLD_MB3_SLC48_HF_SBREF_0013: H>>F
13: EP2D_BOLD_MB3_SLC48_SBREF_0011: F>>H
14: EP2D_BOLD_MB4_SLC48_0010: F>>H
15: EP2D_BOLD_MB4_SLC48_SBREF_0009: F>>H
/ your_study_folder_path/PhantData/BOLDSLICEORDER_Prisma1
1: CMRR_BOLD_AP_MB1_46SLC_FH_0002: F>>H
2: CMRR_BOLD_AP_MB1_46SLC_HF_0003: H>>F
3: CMRR_BOLD_AP_MB3_48SLC_FH_0009: F>>H
4: CMRR_BOLD_AP_MB3_48SLC_FH_SBREF_0008: F>>H
5: CMRR_BOLD_AP_MB3_48SLC_HF_0011: H>>F
6: CMRR_BOLD_AP_MB3_48SLC_HF_SBREF_0010: H>>F
7: CMRR_BOLD_AP_MB4_48SLC_FH_0005: F>>H
8: CMRR_BOLD_AP_MB4_48SLC_FH_SBREF_0004: F>>H
9: CMRR_BOLD_AP_MB4_48SLC_HF_0007: H>>F
10: CMRR_BOLD_AP_MB4_48SLC_HF_SBREF_0006: H>>F
11: MGH_BOLD_AP_MB1_46SLC_FH_0012: F>>H
12: MGH_BOLD_AP_MB1_46SLC_FH_PMU_0013: F>>H
13: MGH_BOLD_AP_MB1_46SLC_HF_0014: H>>F
14: MGH_BOLD_AP_MB1_46SLC_HF_PMU_0015: H>>F
15: MGH_BOLD_AP_MB3_48SLC_FH_0020: F>>H
16: MGH_BOLD_AP_MB3_48SLC_FH_PMU_0021: F>>H
17: MGH_BOLD_AP_MB3_48SLC_HF_0022: H>>F
18: MGH_BOLD_AP_MB3_48SLC_HF_PMU_0023: H>>F
19: MGH_BOLD_AP_MB4_48SLC_FH_0016: F>>H
20: MGH_BOLD_AP_MB4_48SLC_FH_PMU_0017: F>>H
21: MGH_BOLD_AP_MB4_48SLC_HF_0018: H>>F
22: MGH_BOLD_AP_MB4_48SLC_HF_PMU_0019: H>>F
23: SIEMENS_BOLD_AP_MB1_46SLC_FH_0024: F>>H
24: SIEMENS_BOLD_AP_MB1_46SLC_HF_0025: H>>F
25: SIEMENS_BOLD_AP_MB3_48SLC_FH_0028: F>>H
26: SIEMENS_BOLD_AP_MB3_48SLC_HF_0029: H>>F
27: SIEMENS_BOLD_AP_MB4_48SLC_FH_0026: F>>H
28: SIEMENS_BOLD_AP_MB4_48SLC_HF_0027: H>>F
