Hello Sir Michael and teams
I already use MITK CL and when reading some of my DICOM folder to convert it
into NRRD using MitkCLDicom2Nrrd module using
https://github.com/MIC-DKFZ/LIDC-IDRI-processing/blob/master/lidc_data_to_nifti.py
code (with some adjustment to read my custom DICOM datasets)
It reads my DICOM patients folder as 3x3D blocks instead of 1x3D blocks
I am sure that image is actually 1 whole 3D blocks, not 3x3D blocks -->
crosschecked at MicroDicom and Aliza
Maybe this clip of CL generated will help to identify the source of problem
Is there a way to read the whole folder as 1 NRRD file instead of reading them
manually 8 steps?
I am eagerly waiting for your answer.
Thank you Sir.
Best Regards,
Ivan William Harsono
Medical Doctor graduate (GP)
Postgraduate computer science student at Bina Nusantara University, Indonesia
Best Regards,
Ivan William Harsono, S.Ked
MitkCLDicom2Nrrd -i "D:\DICOM_Moscow\+AGFA000000005675_AGFA000000005658\+5_Lung
1.0 Vol" -o
"D:\Moscow_NRRD\nrrd_file\AGFA000000005675b\AGFA000000005675b_ct_scan.nrrd"
Running Command Line Utility *Dicom Loader*
Sat Apr 13 22:50:59 2019
0.29 core.mod.core.ioMimetypes: DICOM Modality is CT
0.30 core.mod.core.ioMimetypes: DICOM Modality is CT
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8257
Physical Memory: Total: 16315 Available: 10165
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.0149162 0.0149162
0.0149162 0.0149162 0
Condensing 3D blocks 1 1.12057e-05 1.12057e-05
1.12057e-05 1.12057e-05 0
EquiDistantBlocksSorter 1 0.00044179 0.00044179
0.00044179 0.00044179 0
Output 1 0.000312805 0.000312805
0.000312805 0.000312805 0
Reset 1 9.53674e-07 9.53674e-07
9.53674e-07 9.53674e-07 0
Sorting frames 1 0.310491 0.310491
0.310491 0.310491 0
Sorting step 0 1 0.0051055 0.0051055
0.0051055 0.0051055 0
Sorting step 1 1 0.00418448 0.00418448
0.00418448 0.00418448 0
---------------------------------------------------------------
3.61 core.mod.dicomReader.dicomFileReaderselector: Reader 0 (Instance Number,
consecutive) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8258
Physical Memory: Total: 16315 Available: 10178
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00448346 0.00448346
0.00448346 0.00448346 0
Condensing 3D blocks 1 1.74046e-05 1.74046e-05
1.74046e-05 1.74046e-05 0
EquiDistantBlocksSorter 1 0.000686646 0.000686646
0.000686646 0.000686646 0
Output 1 0.000232458 0.000232458
0.000232458 0.000232458 0
Reset 1 7.15256e-07 7.15256e-07
7.15256e-07 7.15256e-07 0
Sorting frames 1 0.311053 0.311053
0.311053 0.311053 0
Sorting step 0 1 0.0054512 0.0054512
0.0054512 0.0054512 0
Sorting step 1 1 0.00415039 0.00415039
0.00415039 0.00415039 0
---------------------------------------------------------------
4.49 core.mod.dicomReader.dicomFileReaderselector: Reader 1 (Instance Number,
non-consecutive) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8256
Physical Memory: Total: 16315 Available: 10177
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00415564 0.00415564
0.00415564 0.00415564 0
Condensing 3D blocks 1 1.12057e-05 1.12057e-05
1.12057e-05 1.12057e-05 0
EquiDistantBlocksSorter 1 0.000781775 0.000781775
0.000781775 0.000781775 0
Output 1 0.000258207 0.000258207
0.000258207 0.000258207 0
Reset 1 7.15256e-07 7.15256e-07
7.15256e-07 7.15256e-07 0
Sorting frames 1 0.311142 0.311142
0.311142 0.311142 0
Sorting step 0 1 0.00478435 0.00478435
0.00478435 0.00478435 0
Sorting step 1 1 0.00455904 0.00455904
0.00455904 0.00455904 0
---------------------------------------------------------------
5.38 core.mod.dicomReader.dicomFileReaderselector: Reader 2 (Slice Location)
suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8261
Physical Memory: Total: 16315 Available: 10178
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00320768 0.00320768
0.00320768 0.00320768 0
Condensing 3D blocks 1 3.48091e-05 3.48091e-05
3.48091e-05 3.48091e-05 0
EquiDistantBlocksSorter 1 0.000711441 0.000711441
0.000711441 0.000711441 0
Output 1 0.000308275 0.000308275
0.000308275 0.000308275 0
Reset 1 7.15256e-07 7.15256e-07
7.15256e-07 7.15256e-07 0
Sorting frames 1 0.325963 0.325963
0.325963 0.325963 0
Sorting step 0 1 0.00450087 0.00450087
0.00450087 0.00450087 0
Sorting step 1 1 0.0200472 0.0200472
0.0200472 0.0200472 0
---------------------------------------------------------------
6.28 core.mod.dicomReader.dicomFileReaderselector: Reader 3 (Image Position)
suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8256
Physical Memory: Total: 16315 Available: 10179
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00483084 0.00483084
0.00483084 0.00483084 0
Condensing 3D blocks 1 1.07288e-05 1.07288e-05
1.07288e-05 1.07288e-05 0
EquiDistantBlocksSorter 1 0.000520706 0.000520706
0.000520706 0.000520706 0
Output 1 0.000301838 0.000301838
0.000301838 0.000301838 0
Reset 1 4.76837e-07 4.76837e-07
4.76837e-07 4.76837e-07 0
Sorting frames 1 0.324256 0.324256
0.324256 0.324256 0
Sorting step 0 1 0.00441647 0.00441647
0.00441647 0.00441647 0
Sorting step 1 1 0.0184202 0.0184202
0.0184202 0.0184202 0
---------------------------------------------------------------
7.19 core.mod.dicomReader.dicomFileReaderselector: Reader 4 (Image Position by
Acquisition) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8258
Physical Memory: Total: 16315 Available: 10171
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00278759 0.00278759
0.00278759 0.00278759 0
Condensing 3D blocks 1 5.10216e-05 5.10216e-05
5.10216e-05 5.10216e-05 0
EquiDistantBlocksSorter 1 0.000638247 0.000638247
0.000638247 0.000638247 0
Output 1 0.000259399 0.000259399
0.000259399 0.000259399 0
Reset 1 4.76837e-07 4.76837e-07
4.76837e-07 4.76837e-07 0
Sorting frames 1 0.324714 0.324714
0.324714 0.324714 0
Sorting step 0 1 0.00530243 0.00530243
0.00530243 0.00530243 0
Sorting step 1 1 0.0179813 0.0179813
0.0179813 0.0179813 0
---------------------------------------------------------------
8.10 core.mod.dicomReader.dicomFileReaderselector: Reader 5 (2013 default
sorting for 3D+t) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8257
Physical Memory: Total: 16315 Available: 10172
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.0032804 0.0032804
0.0032804 0.0032804 0
Condensing 3D blocks 1 3.19481e-05 3.19481e-05
3.19481e-05 3.19481e-05 0
EquiDistantBlocksSorter 1 0.000468731 0.000468731
0.000468731 0.000468731 0
Output 1 0.000292301 0.000292301
0.000292301 0.000292301 0
Reset 1 7.15256e-07 7.15256e-07
7.15256e-07 7.15256e-07 0
Sorting frames 1 0.325689 0.325689
0.325689 0.325689 0
Sorting step 0 1 0.00569582 0.00569582
0.00569582 0.00569582 0
Sorting step 1 1 0.0187731 0.0187731
0.0187731 0.0187731 0
---------------------------------------------------------------
9.11 core.mod.dicomReader.dicomFileReaderselector: Reader 6 (IPP 3D+t) suggests
3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8255
Physical Memory: Total: 16315 Available: 10172
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00329757 0.00329757
0.00329757 0.00329757 0
Condensing 3D blocks 1 5.10216e-05 5.10216e-05
5.10216e-05 5.10216e-05 0
EquiDistantBlocksSorter 1 0.000438213 0.000438213
0.000438213 0.000438213 0
Output 1 0.000228405 0.000228405
0.000228405 0.000228405 0
Reset 1 1.19209e-06 1.19209e-06
1.19209e-06 1.19209e-06 0
Sorting frames 1 0.324465 0.324465
0.324465 0.324465 0
Sorting step 0 1 0.00507307 0.00507307
0.00507307 0.00507307 0
Sorting step 1 1 0.0183446 0.0183446
0.0183446 0.0183446 0
---------------------------------------------------------------
10.00 core.mod.dicomReader.dicomFileReaderselector: Reader 7 (3D+t by
AcquisitionNumber) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8256
Physical Memory: Total: 16315 Available: 10171
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00260687 0.00260687
0.00260687 0.00260687 0
Condensing 3D blocks 1 3.29018e-05 3.29018e-05
3.29018e-05 3.29018e-05 0
EquiDistantBlocksSorter 1 0.000457525 0.000457525
0.000457525 0.000457525 0
Output 1 0.000225067 0.000225067
0.000225067 0.000225067 0
Reset 1 1.19209e-06 1.19209e-06
1.19209e-06 1.19209e-06 0
Sorting frames 1 0.323678 0.323678
0.323678 0.323678 0
Sorting step 0 1 0.00439382 0.00439382
0.00439382 0.00439382 0
Sorting step 1 1 0.0182056 0.0182056
0.0182056 0.0182056 0
---------------------------------------------------------------
10.88 core.mod.dicomReader.dicomFileReaderselector: Reader 8 (3D+t by
TriggerTime) suggests 3 3D blocks
---------------------------------------------------------------
System: ASUSDESKTOP
Processor: Unknown P6 family
Cache: -1
Clock: 3599.00
Physical CPUs: 4
Logical CPUs: 8
Virtual Memory: Total: 18747 Available: 8254
Physical Memory: Total: 16315 Available: 10170
OSName: Windows
Release: Professional
Version: (Build 9200)
Platform: AMD64
Operating System is 64 bit
ITK Version: 4.13.0
Name Of Probe (Time) Iterations Total (s) Min (s) Mean
(s) Max (s) StdDev (s)
Check input for DCM 1 0.00190854 0.00190854
0.00190854 0.00190854 0
Condensing 3D blocks 1 1.38283e-05 1.38283e-05
1.38283e-05 1.38283e-05 0
EquiDistantBlocksSorter 1 0.00134015 0.00134015
0.00134015 0.00134015 0
Output 1 0.000398159 0.000398159
0.000398159 0.000398159 0
Reset 1 1.19209e-05 1.19209e-05
1.19209e-05 1.19209e-05 0
Sorting frames 1 0.313246 0.313246
0.313246 0.313246 0
Sorting step 0 1 0.00531507 0.00531507
0.00531507 0.00531507 0
Sorting step 1 1 0.00566459 0.00566459
0.00566459 0.00566459 0
---------------------------------------------------------------
22.39 core.mod.core.imgIo: Writing image:
D:/Moscow_NRRD/nrrd_file/AGFA000000005675b/AGFA000000005675b_ct_scan.nrrd
22.43 core.mod.core.imgIo: Writing image:
D:/Moscow_NRRD/nrrd_file/AGFA000000005675b/AGFA000000005675b_ct_scan_1.nrrd
24.56 core.mod.core.imgIo: Writing image:
D:/Moscow_NRRD/nrrd_file/AGFA000000005675b/AGFA000000005675b_ct_scan_2.nrrd_______________________________________________
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