Instruments

1: RC MILabsU-CT

2: MR Solutions 3T & 7T MRI

3: Siemens ARTIS pheno

1 - RC MILabsU-CT

The microCT data needed to be transferred to the RDS before uploading from RDS to XNAT. Both XNAT and RDS will keep a copy of microCT data at the current stage. If RDS storage researches its maximum capacity or budget in the future, the microCT data on RDS will be removed periodically to save the space.

The microCT data can be categorized into three types: raw data, temporary data and reconstructed data.

The raw data is saved on the acquisition computer, and in the D drive of the reconstruction computer.

The temporary data is generated in the reconstruction process including the “corr” and “prev” folder of each scan and saved in the “ct-data” folder. “corr” folder contains all the projection correction files, while “prev” folder contains the single slice preview image of reconstruction. “corr” and “prev” folder will not be uploaded to the RDS and XNAT.

The reconstructed data contains the final images for CT reconstruction, and it is saved in the “Results” folder of each scan. Data is uploaded from microCT to RDS daily at 7 p.m.

The screenshot above is the acquisition control screen. The User field should always leave blank. The Study field should be filled with the XNAT Project ID and Subject Name in XNAT, e.g. 123_SubjectName.

Project name can’t contain _, this symbol is used to separate the Project ID and Subject Name. Subject Name can contain any numbers of _.

The Scan name will become the Session name on XNAT.

Instrument data hierarchy is:

Z: (Aquisiton) D: (Reconstruction)

D:\Data\[Study]\[Scan]\*

[Study] is [XNAT Project ID]_[Subject] [Scan] is [Date]_[Other]

Metadata

Instrument Source	Logic	Config Source	XNAT Destination
`[Study]`	`[XNAT Project ID]_*`	-	Subject
`[Study]`	`*_[Subject]`		Subject
`[Scan]`	-	-	Session
-	-	TBD	`[IID]`
-	-	TBD	`[QCPID]`
`[Scan]`	`[Date]_*`	-	Date
-	-	-	Time
`[Scan].log`	`…User: [Operator]…` (Not collecting this for now)	-	Operator
-	-	TBD	Scanner Name
-	-	TBD	Scanner Type
-	-	Sydney Imaging	Acquisition Site

Data

Original structure	Note	XNAT structure	XNAT File Type
`[Scan].ct-sequence`		`[Scan].zip`	uct	RAW
`[Scan].zipuct`		`[Scan].zip`	uct	RAW
`[Scan].mCT`		`[Scan].zip`	uct	RAW
`[Scan].parameters`		`[Scan].zip`	uct	RAW
`[Scan].log`		`[Scan].zip`	uct	RAW
`[Scan].comments`		`[Scan].zip`	uct	RAW
`[Scan]_left.png`		`[Scan].zip`	uct	RAW
`[Scan]_right.png`		`[Scan].zip`	uct	RAW
`[Scan]_top.png`		`[Scan].zip`	uct	RAW
`[Scan]_x-ray-left.png`		`[Scan].zip`	uct	RAW
`[Scan]_x-ray-right.png`		`[Scan].zip`	uct	RAW
`[Scan]_x-ray-top.png`		`[Scan].zip`	uct	RAW
`ct-data/calibration/[Stuff].smv`			calibration
`ct-data/calibration/[stuff2]_dark.tif`			calibration
`ct-data/calibration/[stuff2]_white.tif`			calibration
`ct-data/calibration/geopar.cfg`			calibration
`ct-data/proj_000_0_log.csv`			proj
`ct-data/proj_000_0_00_[NNN].tif`	where NNN is the index		proj
`Results/CT_[Scan]_80um.log`	Not maintaining folder structure	`CT_[Scan]_80um.log`	log	RECON
`Results/CT_[Scan]_80um.nii`	Not maintaining folder structure	`CT_[Scan]_80um.nii`	NIFTI	RECON

2 - MR Solutions 3T & 7T MRI

[Series ID] should be used for matching files.

The Project field should filled with the XNAT shortcode (EZBooking Project ID) and the Subject field will be filled with the project name.

Note

For the new project created through DashR, the XNAT shortcode should be at least 3 digits/characters and less than 20 digits/characters.

If less than 3 digits, zeros should be added at the beginning. For example, XNAT shortcode 044 for EZBooking Project ID 44

Metadata

Instrument Source	Logic	Config Source	XNAT Destination
(0010,0010)	`[Project]:*`	-	`[Project]`
(0010,0010)	`*:[Subject]`	-	`[Subject]`
(0008,0020)	`[YYYYMMDD]`		`[Session]`
(0008,0050)	[Subject Accession Number]	-
-	-	3T: 10.25910/5cf9e65ffa8c4 7T: 10.25910/5cf9f821b4c94	[IID] TBD
-	-	TBD	[QCPID] TBD
TBC	-	-	Date
Timestamp (0008,0032) TBC	-	-	Time
Acquisition Duration (0018,9073)	-	-	TBD
Protocol Name (0018,1030) /Sequence Name (0018,0024)	-	-	TBD
-	-	-	Operator
(0008,1010) Station Name	-	-	Scanner Name
(0008,1090) Manufacturer’s Model Name	-	-	Scanner Type
-	-	Sydney Imaging	Acquisition Site

Data

Original structure	Note	XNAT structure	XNAT File Type
`D:\smis\dev\Data\[Subject ID]\DICOM\[Series]\[1]\[Series]_[ScanX]`	DICOM	`\Session\[Series]\`	DICOM
`D:\smis\dev\Data\[Subject ID]\Image\[Series]\[1]\[Series]_[ScanX]`	SUR	`\Session\[Series]\`	SUR
`D:\smis\dev\Data\[Subject ID]\Image\[Series]\patient[SubjectID]_scan[Series]`	PET (log)
`D:\smis\dev\Data\[Subject ID]\Image\[Series]\[Reconstruction]\[Series]_stuff`	PET (Reconstructed)
`D:\smis\dev\Data\[Subject ID]\Spectroscopy\[Series]\[Series]_0`	Spectroscopy	`\Session\[Series]\`	MRD, SPR
`D:\smis\dev\MRD\[Subject ID]\Image\[Series]\[Series]_0`	MRD, RPR, rtv	`\Session\[Series]\`	MRD, RPR
`D:\smis\dev\MRD\[Subject ID]\Image\[Series]\[Series]_0_o`	MRD, RPR, rtv	`\Session\[Series]\`	MRD, RPR
`D:\smis\dev\MRD\[Subject ID]\Image\[Series]\btable.txt`	MRD, RPR, rtv	`\Session\[Series]\`	btable
`D:\smis\dev\MRD\[Subject ID]\Image\[Series]\rtable.txt`	MRD, RPR, rtv	`\Session\[Series]\`	rtable
`D:\smis\dev\PetRaw\[Subject ID]\[Series]\pet_[Series]`	PET (RAW)

3 - Siemens ARTIS pheno

Metadata

Instrument Source	Logic	Config Source	XNAT Destination
Additional Info field: Project:HT-003	(0010,4000) Patient’s Comments	(0010,4000) Patient’s Comments	Project: HT-003
Lastname:Mukherjee Firstname:Sheep1 Title:	(0010,0010) Patient’s Name	(0010,0010) Patient’s Name	Subject: Mukherjee_sheep1
Patient ID: Patient01	(0010,0020) Patient ID	(0010,0020) Patient ID + (0032,0012) Study ID Issuer	Session: Patient01_210301-15_47_19-DST-IVS
	(0020,0010) Study UID	(0020,0010) Study UID	SCAN ID: 990
		10.25910/5cf9f821b4c94	`[IID]` TBD
			`[QCPID]` TBD

[Path] needs to be determined. It can be on instrument, or the export location on RDS.

Data

Original structure	Note	XNAT structure
`[Path]//[File].jpg`	To be covered with DICOM2JPEG	Resource file
`[Path]//[File].avi`		Resource file
`[Path]//[File].txt`		Resource file
`[Path]//[File].csv`		Resource file