Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1657 closed defect (nonchimerax)

DICOM singular matrix error

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: moderate Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Narrowed this one down to a subset of the QIN LUNG CT data. Zip file attached. Prioritize as you like!

open R0098 format dicomTraceback (most recent call last):

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 252, in execute

cmd.run(cmd_text)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2615, in run

result = ci.function(session, kw_args)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open

from_database=from_database, ignore_cache=ignore_cache, kw))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open

models = handle_unknown_kw(session.models.open, paths, format=format, name=name, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw

return f(*args, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/models.py", line 598, in open

session, filenames, format=format, name=name, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/io.py", line 456, in open_multiple_data

models, status = open_func(session, paths, mname, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 3450, in open_map_format

return open_map(session, stream, name=name, format=format, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/volume.py", line 3066, in open_map

verbose = kw.get('verbose'))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/fileformats.py", line 141, in open_file

data = module.open(apath, kw)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/init.py", line 20, in open

return dicom_grids(paths, log = log, verbose = verbose)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_grid.py", line 43, in dicom_grids

g = DicomGrid(d)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/dicom/dicom_grid.py", line 58, in init

file_type = 'dicom', time = time, channel = channel)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 100, in init

self.update_transform()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 186, in update_transform

tf, tf_inv = transformation_and_inverse(self.origin, self.step, rsaxes)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/griddata.py", line 428, in transformation_and_inverse

tf_inv = tf.inverse()

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/geometry/place.py", line 187, in inverse

self._inverse = Place(m34.invert_matrix(self._matrix))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/geometry/matrix.py", line 130, in invert_matrix

rinv[:, :] = matrix_inverse(r)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 551, in inv

ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 97, in _raise_linalgerror_singular

raise LinAlgError("Singular matrix")

numpy.linalg.LinAlgError: Singular matrix

numpy.linalg.LinAlgError: Singular matrix

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 97, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")

Attachments (1)

R0098.zip​ (25.2 MB ) - added by Elaine Meng 7 years ago.

Change History (5)

by Elaine Meng, 7 years ago

Attachment: R0098.zip​ added

comment:1 by Tom Goddard, 7 years ago

Resolution: → nonchimerax
Status: assigned → closed

This DICOM data set has 88 planes, 87 of which are spaced at 4 mm in z but one spacing is 0. The two planes with spacing 0 belong to the same series and instance number 87 and 88 and none of the dicom meta data indicates what is going on. Both plane images look identical. Running diff on the dicom metadata read by pydicom gives no indication that either of these planes is special.

So the data set just looks bad to me. I've put in error check code that warns when the plane spacing is not uniform and then uses the maximum plane spacing and outputs all the plane positions. So at least the data can be opened.

$ diff ~/Desktop/meta0 ~/Desktop/meta1
4c4
< (0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.121164085244453070955521073799
---

(0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.291193578318052300432936075538

12c12
< (0008, 0033) Content Time TM: '110741.462407'
---

(0008, 0033) Content Time TM: '111326.625000'

32,34c32,33
< (0009, 0010) Private Creator LO: 'SIEMENS CT VA1 DUMMY'
< (0009, 0011) Private Creator LO: 'SPI RELEASE 1'
< (0009, 0012) Private Creator LO: 'EMAGEON STUDY HOME'
---

(0009, 0010) Private Creator LO: 'SPI RELEASE 1'
(0009, 0011) Private Creator LO: 'EMAGEON STUDY HOME'

109,110d107
< (0019, 0010) Private Creator LO: 'SIEMENS CT VA0 COAD'
< (0019, 10b0) [Feed per Rotation] UN: b'18'
116c113
< (0020, 0013) Instance Number IS: "87"
---

(0020, 0013) Instance Number IS: "88"

124,125d120
< (0021, 0010) Private Creator LO: 'SIEMENS MED'
< (0021, 1011) [Target] UN: b'-8
0'

ChimeraX debug output:

Plane z spacings are unequal, min = 0, max = 4, using max.
000085.dcm (-212.59961, -355.59961, 69.9)
000057.dcm (-212.59961, -355.59961, 69.9)
000030.dcm (-212.59961, -355.59961, 73.9)
000087.dcm (-212.59961, -355.59961, 77.9)
000011.dcm (-212.59961, -355.59961, 81.9)
000054.dcm (-212.59961, -355.59961, 85.9)
000021.dcm (-212.59961, -355.59961, 89.9)
000015.dcm (-212.59961, -355.59961, 93.9)
000040.dcm (-212.59961, -355.59961, 97.9)
000012.dcm (-212.59961, -355.59961, 101.9)
000066.dcm (-212.59961, -355.59961, 105.9)
000086.dcm (-212.59961, -355.59961, 109.9)
000016.dcm (-212.59961, -355.59961, 113.9)
000051.dcm (-212.59961, -355.59961, 117.9)
000002.dcm (-212.59961, -355.59961, 121.9)
000053.dcm (-212.59961, -355.59961, 125.9)
000045.dcm (-212.59961, -355.59961, 129.9)
000010.dcm (-212.59961, -355.59961, 133.9)
000024.dcm (-212.59961, -355.59961, 137.9)
000000.dcm (-212.59961, -355.59961, 141.9)
000060.dcm (-212.59961, -355.59961, 145.9)
000023.dcm (-212.59961, -355.59961, 149.9)
000055.dcm (-212.59961, -355.59961, 153.9)
000074.dcm (-212.59961, -355.59961, 157.9)
000034.dcm (-212.59961, -355.59961, 161.9)
000001.dcm (-212.59961, -355.59961, 165.9)
000042.dcm (-212.59961, -355.59961, 169.9)
000044.dcm (-212.59961, -355.59961, 173.9)
000004.dcm (-212.59961, -355.59961, 177.9)
000025.dcm (-212.59961, -355.59961, 181.9)
000027.dcm (-212.59961, -355.59961, 185.9)
000043.dcm (-212.59961, -355.59961, 189.9)
000014.dcm (-212.59961, -355.59961, 193.9)
000006.dcm (-212.59961, -355.59961, 197.9)
000064.dcm (-212.59961, -355.59961, 201.9)
000058.dcm (-212.59961, -355.59961, 205.9)
000076.dcm (-212.59961, -355.59961, 209.9)
000018.dcm (-212.59961, -355.59961, 213.9)
000070.dcm (-212.59961, -355.59961, 217.9)
000026.dcm (-212.59961, -355.59961, 221.9)
000059.dcm (-212.59961, -355.59961, 225.9)
000065.dcm (-212.59961, -355.59961, 229.9)
000079.dcm (-212.59961, -355.59961, 233.9)
000046.dcm (-212.59961, -355.59961, 237.9)
000078.dcm (-212.59961, -355.59961, 241.9)
000013.dcm (-212.59961, -355.59961, 245.9)
000036.dcm (-212.59961, -355.59961, 249.9)
000038.dcm (-212.59961, -355.59961, 253.9)
000062.dcm (-212.59961, -355.59961, 257.9)
000083.dcm (-212.59961, -355.59961, 261.9)
000022.dcm (-212.59961, -355.59961, 265.9)
000071.dcm (-212.59961, -355.59961, 269.9)
000047.dcm (-212.59961, -355.59961, 273.9)
000080.dcm (-212.59961, -355.59961, 277.9)
000084.dcm (-212.59961, -355.59961, 281.9)
000017.dcm (-212.59961, -355.59961, 285.9)
000041.dcm (-212.59961, -355.59961, 289.9)
000020.dcm (-212.59961, -355.59961, 293.9)
000007.dcm (-212.59961, -355.59961, 297.9)
000005.dcm (-212.59961, -355.59961, 301.9)
000029.dcm (-212.59961, -355.59961, 305.9)
000039.dcm (-212.59961, -355.59961, 309.9)
000075.dcm (-212.59961, -355.59961, 313.9)
000068.dcm (-212.59961, -355.59961, 317.9)
000061.dcm (-212.59961, -355.59961, 321.9)
000033.dcm (-212.59961, -355.59961, 325.9)
000069.dcm (-212.59961, -355.59961, 329.9)
000037.dcm (-212.59961, -355.59961, 333.9)
000019.dcm (-212.59961, -355.59961, 337.9)
000050.dcm (-212.59961, -355.59961, 341.9)
000081.dcm (-212.59961, -355.59961, 345.9)
000072.dcm (-212.59961, -355.59961, 349.9)
000073.dcm (-212.59961, -355.59961, 353.9)
000031.dcm (-212.59961, -355.59961, 357.9)
000035.dcm (-212.59961, -355.59961, 361.9)
000077.dcm (-212.59961, -355.59961, 365.9)
000067.dcm (-212.59961, -355.59961, 369.9)
000048.dcm (-212.59961, -355.59961, 373.9)
000003.dcm (-212.59961, -355.59961, 377.9)
000049.dcm (-212.59961, -355.59961, 381.9)
000082.dcm (-212.59961, -355.59961, 385.9)
000052.dcm (-212.59961, -355.59961, 389.9)
000056.dcm (-212.59961, -355.59961, 393.9)
000063.dcm (-212.59961, -355.59961, 397.9)
000009.dcm (-212.59961, -355.59961, 401.9)
000008.dcm (-212.59961, -355.59961, 405.9)
000028.dcm (-212.59961, -355.59961, 409.9)
000032.dcm (-212.59961, -355.59961, 413.9)
Opened 20010413, grid size 512,512,88, pixel 0.801,0.801,4, shown at step 1, values float32

comment:2 by Tom Goddard, 7 years ago

Here is full dicom meta data for the two planes that are at the same z position.

File 000085.dcm

(0008, 0005) Specific Character Set CS: 'ISO_IR 100'
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']
(0008, 0016) SOP Class UID UI: CT Image Storage
(0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.121164085244453070955521073799
(0008, 0020) Study Date DA: '20010413'
(0008, 0021) Series Date DA: '20010413'
(0008, 0022) Acquisition Date DA: '20010413'
(0008, 0023) Content Date DA: '20010413'
(0008, 0030) Study Time TM: '110517.0000'
(0008, 0031) Series Time TM: '111058.0000'
(0008, 0032) Acquisition Time TM: '110741.462407'
(0008, 0033) Content Time TM: '110741.462407'
(0008, 0040) Data Set Type US: 0
(0008, 0041) Data Set Subtype LO: 'IMA NONE'
(0008, 0050) Accession Number SH: '2872091429260497'
(0008, 0054) Retrieve AE Title AE: 'AE_TITLE'
(0008, 0060) Modality CS: 'CT'
(0008, 0070) Manufacturer LO: 'SIEMENS'
(0008, 0090) Referring Physician's Name PN:
(0008, 1030) Study Description LO:
(0008, 103e) Series Description LO:
(0008, 1080) Admitting Diagnoses Description LO:
(0008, 1090) Manufacturer's Model Name LO: 'Sensation 16'
(0008, 1140) Referenced Image Sequence 1 item(s) ----
(0008, 1150) Referenced SOP Class UID UI: CT Image Storage
(0008, 1155) Referenced SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.193536268399286295609105791636

(0008, 2112) Source Image Sequence 1 item(s) ----
(0008, 1150) Referenced SOP Class UID UI: CT Image Storage
(0008, 1155) Referenced SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.379458909613810955889171368547

(0009, 0010) Private Creator LO: 'SIEMENS CT VA1 DUMMY'
(0009, 0011) Private Creator LO: 'SPI RELEASE 1'
(0009, 0012) Private Creator LO: 'EMAGEON STUDY HOME'
(0010, 0010) Patient's Name PN: 'R0098'
(0010, 0020) Patient ID LO: 'R0098'
(0010, 0030) Patient's Birth Date DA:
(0010, 0040) Patient's Sex CS: 'O'
(0010, 1010) Patient's Age AS:
(0010, 1020) Patient's Size DS:
(0010, 1030) Patient's Weight DS:
(0010, 2160) Ethnic Group SH:
(0010, 2180) Occupation SH:
(0010, 21b0) Additional Patient History LT:
(0010, 21c0) Pregnancy Status US: 4
(0010, 4000) Patient Comments LT:
(0011, 0010) Private Creator LO: 'SPI RELEASE 1'
(0011, 1010) [Organ] UN: b'CT Thorax w/Cont'
(0012, 0062) Patient Identity Removed CS: 'YES'
(0012, 0063) De-identification Method LO: 'Per DICOM PS 3.15 AnnexE. Details in 0012,0064'
(0012, 0064) De-identification Method Code Sequence 8 item(s) ----
(0008, 0100) Code Value SH: '113100'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Basic Application Confidentiality Profile'

(0008, 0100) Code Value SH: '113101'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Pixel Data Option'

(0008, 0100) Code Value SH: '113104'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Structured Content Option'

(0008, 0100) Code Value SH: '113105'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Descriptors Option'

(0008, 0100) Code Value SH: '113107'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Longitudinal Temporal Information Modified Dates Option'

(0008, 0100) Code Value SH: '113108'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Patient Characteristics Option'

(0008, 0100) Code Value SH: '113109'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Device Identity Option'

(0008, 0100) Code Value SH: '113111'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Safe Private Option'

(0013, 0010) Private Creator LO: 'CTP'
(0013, 1010) Private tag data UN: b'QIN LUNG CT '
(0013, 1013) Private tag data UN: b'43207015'
(0018, 0015) Body Part Examined CS: 'LUNG'
(0018, 0050) Slice Thickness DS: "4"
(0018, 0060) KVP DS: "120"
(0018, 0090) Data Collection Diameter DS: "500"
(0018, 1020) Software Version(s) LO: 'VA70C'
(0018, 1030) Protocol Name LO:
(0018, 1100) Reconstruction Diameter DS: "410"
(0018, 1110) Distance Source to Detector DS: "1040"
(0018, 1111) Distance Source to Patient DS: "570"
(0018, 1120) Gantry/Detector Tilt DS: "0"
(0018, 1130) Table Height DS: "151"
(0018, 1140) Rotation Direction CS: 'CW'
(0018, 1150) Exposure Time IS: "500"
(0018, 1151) X-Ray Tube Current IS: "168"
(0018, 1152) Exposure IS: "112"
(0018, 1160) Filter Type SH: '0'
(0018, 1170) Generator Power IS: "23"
(0018, 1190) Focal Spot(s) DS: "0.7"
(0018, 1200) Date of Last Calibration DA: '20010413'
(0018, 1201) Time of Last Calibration TM: '080655.000000'
(0018, 1210) Convolution Kernel SH: 'B40f'
(0018, 5100) Patient Position CS: 'HFS'
(0019, 0010) Private Creator LO: 'SIEMENS CT VA0 COAD'
(0019, 10b0) [Feed per Rotation] UN: b'18'
(0020, 000d) Study Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.378450399989714541022204301518
(0020, 000e) Series Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.729243044254570583133005972993
(0020, 0010) Study ID SH:
(0020, 0011) Series Number IS: "3"
(0020, 0012) Acquisition Number IS: "2"
(0020, 0013) Instance Number IS: "87"
(0020, 0032) Image Position (Patient) DS: ['-212.59961', '-355.59961', '69.9']
(0020, 0037) Image Orientation (Patient) DS: ['1', '0', '0', '0', '1', '0']
(0020, 0052) Frame of Reference UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.281949768489412648962353822266
(0020, 1002) Images in Acquisition IS: "0"
(0020, 1040) Position Reference Indicator LO:
(0020, 1041) Slice Location DS: "69.9"
(0020, 4000) Image Comments LT:
(0021, 0010) Private Creator LO: 'SIEMENS MED'
(0021, 1011) [Target] UN: b'-8
0'
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0006) Planar Configuration US: 0
(0028, 0010) Rows US: 512
(0028, 0011) Columns US: 512
(0028, 0030) Pixel Spacing DS: ['0.80078125', '0.80078125']
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 12
(0028, 0102) High Bit US: 11
(0028, 0103) Pixel Representation US: 0
(0028, 0106) Smallest Image Pixel Value US: 0
(0028, 0107) Largest Image Pixel Value US: 0
(0028, 0303) Longitudinal Temporal Information M CS: 'MODIFIED'
(0028, 1050) Window Center DS: "20.0"
(0028, 1051) Window Width DS: "400.0"
(0028, 1052) Rescale Intercept DS: "-1024"
(0028, 1053) Rescale Slope DS: "1"
(0028, 1055) Window Center & Width Explanation LO: ['WINDOW1', 'WINDOW2']
(0029, 0010) Private Creator LO: 'SIEMENS CSA HEADER'
(0029, 0011) Private Creator LO: 'SIEMENS MEDCOM HEADER'
(0032, 000a) Study Status ID CS: 'COMPLETED'
(0032, 000c) Study Priority ID CS: 'LOW'
(0032, 1030) Reason for Study LO:
(0032, 1060) Requested Procedure Description LO: 'CT Thorax w/Cont'
(0032, 4000) Study Comments LT:
(0091, 0010) Private Creator LO: 'SIENET'
(0095, 0010) Private Creator LO: 'SIENET'
(0099, 0010) Private Creator LO: 'SIENET'
(0099, 1002) [Key Images] UN: b'\x00\x00\x00\x00'
(7fe0, 0010) Pixel Data OW: Array of 524288 bytes

File 000057.dcm

(0008, 0005) Specific Character Set CS: 'ISO_IR 100'
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL', 'CT_SOM5 SPI']
(0008, 0016) SOP Class UID UI: CT Image Storage
(0008, 0018) SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.291193578318052300432936075538
(0008, 0020) Study Date DA: '20010413'
(0008, 0021) Series Date DA: '20010413'
(0008, 0022) Acquisition Date DA: '20010413'
(0008, 0023) Content Date DA: '20010413'
(0008, 0030) Study Time TM: '110517.0000'
(0008, 0031) Series Time TM: '111058.0000'
(0008, 0032) Acquisition Time TM: '110741.462407'
(0008, 0033) Content Time TM: '111326.625000'
(0008, 0040) Data Set Type US: 0
(0008, 0041) Data Set Subtype LO: 'IMA NONE'
(0008, 0050) Accession Number SH: '2872091429260497'
(0008, 0054) Retrieve AE Title AE: 'AE_TITLE'
(0008, 0060) Modality CS: 'CT'
(0008, 0070) Manufacturer LO: 'SIEMENS'
(0008, 0090) Referring Physician's Name PN:
(0008, 1030) Study Description LO:
(0008, 103e) Series Description LO:
(0008, 1080) Admitting Diagnoses Description LO:
(0008, 1090) Manufacturer's Model Name LO: 'Sensation 16'
(0008, 1140) Referenced Image Sequence 1 item(s) ----
(0008, 1150) Referenced SOP Class UID UI: CT Image Storage
(0008, 1155) Referenced SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.193536268399286295609105791636

(0008, 2112) Source Image Sequence 1 item(s) ----
(0008, 1150) Referenced SOP Class UID UI: CT Image Storage
(0008, 1155) Referenced SOP Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.379458909613810955889171368547

(0009, 0010) Private Creator LO: 'SPI RELEASE 1'
(0009, 0011) Private Creator LO: 'EMAGEON STUDY HOME'
(0010, 0010) Patient's Name PN: 'R0098'
(0010, 0020) Patient ID LO: 'R0098'
(0010, 0030) Patient's Birth Date DA:
(0010, 0040) Patient's Sex CS: 'O'
(0010, 1010) Patient's Age AS:
(0010, 1020) Patient's Size DS:
(0010, 1030) Patient's Weight DS:
(0010, 2160) Ethnic Group SH:
(0010, 2180) Occupation SH:
(0010, 21b0) Additional Patient History LT:
(0010, 21c0) Pregnancy Status US: 4
(0010, 4000) Patient Comments LT:
(0011, 0010) Private Creator LO: 'SPI RELEASE 1'
(0011, 1010) [Organ] UN: b'CT Thorax w/Cont'
(0012, 0062) Patient Identity Removed CS: 'YES'
(0012, 0063) De-identification Method LO: 'Per DICOM PS 3.15 AnnexE. Details in 0012,0064'
(0012, 0064) De-identification Method Code Sequence 8 item(s) ----
(0008, 0100) Code Value SH: '113100'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Basic Application Confidentiality Profile'

(0008, 0100) Code Value SH: '113101'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Pixel Data Option'

(0008, 0100) Code Value SH: '113104'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Structured Content Option'

(0008, 0100) Code Value SH: '113105'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Clean Descriptors Option'

(0008, 0100) Code Value SH: '113107'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Longitudinal Temporal Information Modified Dates Option'

(0008, 0100) Code Value SH: '113108'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Patient Characteristics Option'

(0008, 0100) Code Value SH: '113109'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Device Identity Option'

(0008, 0100) Code Value SH: '113111'
(0008, 0102) Coding Scheme Designator SH: 'DCM'
(0008, 0104) Code Meaning LO: 'Retain Safe Private Option'

(0013, 0010) Private Creator LO: 'CTP'
(0013, 1010) Private tag data UN: b'QIN LUNG CT '
(0013, 1013) Private tag data UN: b'43207015'
(0018, 0015) Body Part Examined CS: 'LUNG'
(0018, 0050) Slice Thickness DS: "4"
(0018, 0060) KVP DS: "120"
(0018, 0090) Data Collection Diameter DS: "500"
(0018, 1020) Software Version(s) LO: 'VA70C'
(0018, 1030) Protocol Name LO:
(0018, 1100) Reconstruction Diameter DS: "410"
(0018, 1110) Distance Source to Detector DS: "1040"
(0018, 1111) Distance Source to Patient DS: "570"
(0018, 1120) Gantry/Detector Tilt DS: "0"
(0018, 1130) Table Height DS: "151"
(0018, 1140) Rotation Direction CS: 'CW'
(0018, 1150) Exposure Time IS: "500"
(0018, 1151) X-Ray Tube Current IS: "168"
(0018, 1152) Exposure IS: "112"
(0018, 1160) Filter Type SH: '0'
(0018, 1170) Generator Power IS: "23"
(0018, 1190) Focal Spot(s) DS: "0.7"
(0018, 1200) Date of Last Calibration DA: '20010413'
(0018, 1201) Time of Last Calibration TM: '080655.000000'
(0018, 1210) Convolution Kernel SH: 'B40f'
(0018, 5100) Patient Position CS: 'HFS'
(0020, 000d) Study Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.378450399989714541022204301518
(0020, 000e) Series Instance UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.729243044254570583133005972993
(0020, 0010) Study ID SH:
(0020, 0011) Series Number IS: "3"
(0020, 0012) Acquisition Number IS: "2"
(0020, 0013) Instance Number IS: "88"
(0020, 0032) Image Position (Patient) DS: ['-212.59961', '-355.59961', '69.9']
(0020, 0037) Image Orientation (Patient) DS: ['1', '0', '0', '0', '1', '0']
(0020, 0052) Frame of Reference UID UI: 1.3.6.1.4.1.14519.5.2.1.4320.7015.281949768489412648962353822266
(0020, 1002) Images in Acquisition IS: "0"
(0020, 1040) Position Reference Indicator LO:
(0020, 1041) Slice Location DS: "69.9"
(0020, 4000) Image Comments LT:
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0006) Planar Configuration US: 0
(0028, 0010) Rows US: 512
(0028, 0011) Columns US: 512
(0028, 0030) Pixel Spacing DS: ['0.80078125', '0.80078125']
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 12
(0028, 0102) High Bit US: 11
(0028, 0103) Pixel Representation US: 0
(0028, 0106) Smallest Image Pixel Value US: 0
(0028, 0107) Largest Image Pixel Value US: 0
(0028, 0303) Longitudinal Temporal Information M CS: 'MODIFIED'
(0028, 1050) Window Center DS: "20.0"
(0028, 1051) Window Width DS: "400.0"
(0028, 1052) Rescale Intercept DS: "-1024"
(0028, 1053) Rescale Slope DS: "1"
(0028, 1055) Window Center & Width Explanation LO: ['WINDOW1', 'WINDOW2']
(0029, 0010) Private Creator LO: 'SIEMENS CSA HEADER'
(0029, 0011) Private Creator LO: 'SIEMENS MEDCOM HEADER'
(0032, 000a) Study Status ID CS: 'COMPLETED'
(0032, 000c) Study Priority ID CS: 'LOW'
(0032, 1030) Reason for Study LO:
(0032, 1060) Requested Procedure Description LO: 'CT Thorax w/Cont'
(0032, 4000) Study Comments LT:
(0091, 0010) Private Creator LO: 'SIENET'
(0095, 0010) Private Creator LO: 'SIENET'
(0099, 0010) Private Creator LO: 'SIENET'
(0099, 1002) [Key Images] UN: b'\x00\x00\x00\x00'
(7fe0, 0010) Pixel Data OW: Array of 524288 bytes

in reply to:  4 comment:3 by Elaine Meng, 7 years ago 

Makes sense to consider it “bad data." I systematically tested all the subdirectories in the QIN LUNG CT study that gave the error, of which there were dozens, and only this one gave the problem.   It will be useful to allow opening all the other un-bad stacks when only one is bad.

in reply to:  5 ; comment:4 by Elaine Meng, 7 years ago 

Horos and 3D Slicer both open that folder without complaint and show an image, but I don’t know how they handled the weirdness with spacing.
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