Opportunistic CT - Revision history

Skboyd: /* DICOM Meta Data */

2026-04-01T18:01:02Z

DICOM Meta Data

← Older revision		Revision as of 18:01, 1 April 2026
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	# Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"		# Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"

	After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).		After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription, etc.).

	I recommend putting them all into a file (I usually call this file "query.txt") instead of having them all on the command line:		I recommend putting them all into a file (I usually call this file "query.txt") instead of having them all on the command line:

Skboyd: /* DICOM Dump */

2026-04-01T18:00:31Z

DICOM Dump

← Older revision		Revision as of 18:00, 1 April 2026
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	Filters to apply to get "just the good stuff":		Filters to apply to get "just the good stuff":
	~~<ul>~~		# Remove anything in group 0002
	Remove anything in group 0002		# Remove anything in odd-numbered groups (private vendor attributes)
	Remove anything in odd-numbered groups (private vendor attributes)		# Remove anything that is indented (these are the nested attributes)
	Remove anything that is indented (these are the nested attributes)		# Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"
	Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"
	~~</ul>~~
	After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).		After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).

Skboyd: /* DICOM Dump */

2026-04-01T17:59:18Z

DICOM Dump

← Older revision		Revision as of 17:59, 1 April 2026
Line 136:		Line 136:

	Filters to apply to get "just the good stuff":		Filters to apply to get "just the good stuff":
			<ul>
	Remove anything in group 0002		Remove anything in group 0002
	Remove anything in odd-numbered groups (private vendor attributes)		Remove anything in odd-numbered groups (private vendor attributes)
	Remove anything that is indented (these are the nested attributes)		Remove anything that is indented (these are the nested attributes)
	Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"		Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"
			</ul>
	After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).		After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).

Skboyd: /* DICOM Dump */

2026-04-01T17:58:39Z

DICOM Dump

Skboyd: /* Calibration */

2026-04-01T17:57:39Z

Calibration

← Older revision		Revision as of 17:57, 1 April 2026
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	[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]		[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]

			==DICOM Meta Data==
			===DICOM Dump===
			If you want a comprehensive list of tags then I suggest "dicomdump" to get output like the following, and then apply some filters:

			(0008,0070) LO "Manufacturer" : [GE MEDICAL SYSTEMS] (18 bytes)
			(0008,0080) LO "InstitutionName" : [FOOTHILLS Hospital] (18 bytes)
			(0008,0090) PN "ReferringPhysicianName" : [] (0 bytes)
			(0008,1010) SH "StationName" : [MRGESEA1] (8 bytes)
			(0008,1030) LO "StudyDescription" : [QUANT MR-(RF_FMC_QUANMR_01_13360)] (34 bytes)
			(0008,103E) LO "SeriesDescription" : [OAx T2-Mapping REG NEW] (22 bytes)
			(0008,1090) LO "ManufacturerModelName" : [DISCOVERY MR750] (16 bytes)
			(0008,1111) SQ "ReferencedPerformedProcedureStepSequence" : (1 item)
			---- SQ Item 0001 at offset 844 ----
			(0008,1150) UI "ReferencedSOPClassUID" : [1.2.840.10008.3.1.2.3.3] {Modality Performed Procedure Step SOP Class} (24 bytes)
			(0008,1155) UI "ReferencedSOPInstanceUID" : [1.2.840.2948978595] (60 bytes)

			Filters to apply to get "just the good stuff":
			Remove anything in group 0002
			Remove anything in odd-numbered groups (private vendor attributes)
			Remove anything that is indented (these are the nested attributes)
			Remove anything that is "UN", "SQ", "OB", "OW", "OF", "OD", "OL", "OV"

			After you've removed all that stuff, you can extract the attributes (e.g. SeriesDescription) etc.).

			I recommend putting them all into a file (I usually call this file "query.txt") instead of having them all on the command line:

			dicomtocsv ./path_to_data -q query.txt -o output.csv

			The query.txt will have contents like this, one attribute per line:

			Manufacturer
			StudyDescription
			SeriesDescription

			I don't recommend using "--default" because future versions of dicomtocsv might change what counts as "default". It's best to list all of the wanted tags explicitly.

Bryn.Matheson: /* Asynchronous calibration */

2025-05-01T21:53:14Z

Asynchronous calibration

← Older revision		Revision as of 21:53, 1 May 2025
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	===Asynchronous calibration===		===Asynchronous calibration===

	This also uses a phantom, but not at the same time as the scan of the patient. Sometimes it can be months or even years away.		This also uses a phantom, but not at the same time as the scan of the patient. Sometimes it can be months or even years away. (This is an ongoing edited section...)

	[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]		[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]

Bryn.Matheson: /* Calibration */

2025-03-07T22:45:17Z

Calibration

← Older revision		Revision as of 22:45, 7 March 2025
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	==Calibration==		==Calibration==
	To ensure accurate material properties and comparability across clinical sites and scanners ~~for~~ quantitative analysis ~~of bone~~ derived from clinical CT scans, the native in-scan Hounsfield Units (HUs) must be converted to their corresponding bone equivalent densities.		To ensure accurate material properties and comparability across clinical sites and scanners during quantitative analysis derived from clinical CT scans, the native in-scan Hounsfield Units (HUs) must be converted to their corresponding bone equivalent densities.

	There are three main types of calibration for CT scans. All of these methods are available in our GitHub repository called [https://github.com/Bonelab/Ogo Ogo].		There are three main types of calibration for CT scans. All of these methods are available in our GitHub repository called [https://github.com/Bonelab/Ogo Ogo].

Bryn.Matheson: /* Phantom calibration */

2025-03-07T22:35:15Z

Phantom calibration

← Older revision		Revision as of 22:35, 7 March 2025
Line 94:		Line 94:

	To run phantom calibration in Ogo, you will need two things:		To run phantom calibration in Ogo, you will need two things:
	1. The raw CT scan (.nii or .nii.gz)		<ol>
	2. A segmentation mask of the phantom rods. Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of		<li>The raw CT scan (.nii or .nii.gz)</li>
	the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.		<li>A segmentation mask of the phantom rods</li>
			</ol>

			Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.

	An example of the phantom rods segmented:		An example of the phantom rods segmented:

Bryn.Matheson: /* Calibration */

2025-03-07T22:32:44Z

Calibration

← Older revision		Revision as of 22:32, 7 March 2025
Line 94:		Line 94:

	To run phantom calibration in Ogo, you will need two things:		To run phantom calibration in Ogo, you will need two things:
	1. The raw CT scan (.nii or .nii.gz)		1. The raw CT scan (.nii or .nii.gz)
	2. A segmentation mask of the phantom rods. Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.		2. A segmentation mask of the phantom rods. Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of
			the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.

	An example of the phantom rods segmented:		An example of the phantom rods segmented:

Bryn.Matheson: /* Phantom calibration */

2025-03-07T22:31:01Z

Phantom calibration

← Older revision		Revision as of 22:31, 7 March 2025
Line 82:		Line 82:
	===Phantom calibration===		===Phantom calibration===

	Phantom calibration is the current imaging gold standard for converting HUs to bone densities. Phantom calibration involves placing a calibration phantom with known density values of either solid CHA or liquid K<sub>2</sub>HPO<sub>4</sub> under the patient in the scan field of view, as seen ~~below.~~		Phantom calibration is the current imaging gold standard for converting HUs to bone densities. Phantom calibration involves placing a calibration phantom with known density values of either solid CHA or liquid K<sub>2</sub>HPO<sub>4</sub> under the patient in the scan field of view, as seen here:

	[[Image:phantom_rods_noseg.png\|600px]]		[[Image:phantom_rods_noseg.png\|600px]]
Line 92:		Line 92:

	where a is the slope of the resulting calibration curve and b is the intercept. This calibration curve is applied to specific bone compartments in the image or to the entire image, creating a bone-equivalent density image. The values of a and b depend on many factors, such as the composition of the X-ray spectrum emitted by the X-ray tube, tube current, reconstruction kernel or table height, and as a result are scanner and image protocol dependent.		where a is the slope of the resulting calibration curve and b is the intercept. This calibration curve is applied to specific bone compartments in the image or to the entire image, creating a bone-equivalent density image. The values of a and b depend on many factors, such as the composition of the X-ray spectrum emitted by the X-ray tube, tube current, reconstruction kernel or table height, and as a result are scanner and image protocol dependent.

			To run phantom calibration in Ogo, you will need two things:
			1. The raw CT scan (.nii or .nii.gz)
			2. A segmentation mask of the phantom rods. Typically, this is done using ITKSnap or some other automated method [TBD], and you segment the inside of the rods, making sure to stop before reaching the edge of the rod to avoid partial volume effects.

			An example of the phantom rods segmented:

			[[Image:phantom_rods_seg.png\|600px]]

	[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]		[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]

← Older revision		Revision as of 17:58, 1 April 2026
Line 123:		Line 123:
	If you want a comprehensive list of tags then I suggest "dicomdump" to get output like the following, and then apply some filters:		If you want a comprehensive list of tags then I suggest "dicomdump" to get output like the following, and then apply some filters:

	(0008,0070) LO "Manufacturer" : [GE MEDICAL SYSTEMS] (18 bytes)		(0008,0070) LO "Manufacturer" : [GE MEDICAL SYSTEMS] (18 bytes)
	(0008,0080) LO "InstitutionName" : [FOOTHILLS Hospital] (18 bytes)		(0008,0080) LO "InstitutionName" : [FOOTHILLS Hospital] (18 bytes)
	(0008,0090) PN "ReferringPhysicianName" : [] (0 bytes)		(0008,0090) PN "ReferringPhysicianName" : [] (0 bytes)
	(0008,1010) SH "StationName" : [MRGESEA1] (8 bytes)		(0008,1010) SH "StationName" : [MRGESEA1] (8 bytes)
	(0008,1030) LO "StudyDescription" : [QUANT MR-(RF_FMC_QUANMR_01_13360)] (34 bytes)		(0008,1030) LO "StudyDescription" : [QUANT MR-(RF_FMC_QUANMR_01_13360)] (34 bytes)
	(0008,103E) LO "SeriesDescription" : [OAx T2-Mapping REG NEW] (22 bytes)		(0008,103E) LO "SeriesDescription" : [OAx T2-Mapping REG NEW] (22 bytes)
	(0008,1090) LO "ManufacturerModelName" : [DISCOVERY MR750] (16 bytes)		(0008,1090) LO "ManufacturerModelName" : [DISCOVERY MR750] (16 bytes)
	(0008,1111) SQ "ReferencedPerformedProcedureStepSequence" : (1 item)		(0008,1111) SQ "ReferencedPerformedProcedureStepSequence" : (1 item)
	---- SQ Item 0001 at offset 844 ----		---- SQ Item 0001 at offset 844 ----
	(0008,1150) UI "ReferencedSOPClassUID" : [1.2.840.10008.3.1.2.3.3] {Modality Performed Procedure Step SOP Class} (24 bytes)		(0008,1150) UI "ReferencedSOPClassUID" : [1.2.840.10008.3.1.2.3.3] {Modality Performed Procedure Step SOP Class} (24 bytes)
	(0008,1155) UI "ReferencedSOPInstanceUID" : [1.2.840.2948978595] (60 bytes)		(0008,1155) UI "ReferencedSOPInstanceUID" : [1.2.840.2948978595] (60 bytes)

	Filters to apply to get "just the good stuff":		Filters to apply to get "just the good stuff":