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Instruments

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.

Acquisition control screen

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 SourceLogicConfig SourceXNAT 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
--TBDScanner Name
--TBDScanner Type
--Sydney ImagingAcquisition Site

Data

Original structureNoteXNAT structureXNAT File Type
[Scan].ct-sequence[Scan].zipuctRAW
[Scan].zipuct[Scan].zipuctRAW
[Scan].mCT[Scan].zipuctRAW
[Scan].parameters[Scan].zipuctRAW
[Scan].log[Scan].zipuctRAW
[Scan].comments[Scan].zipuctRAW
[Scan]_left.png[Scan].zipuctRAW
[Scan]_right.png[Scan].zipuctRAW
[Scan]_top.png[Scan].zipuctRAW
[Scan]_x-ray-left.png[Scan].zipuctRAW
[Scan]_x-ray-right.png[Scan].zipuctRAW
[Scan]_x-ray-top.png[Scan].zipuctRAW
ct-data/calibration/[Stuff].smvcalibration
ct-data/calibration/[stuff2]_dark.tifcalibration
ct-data/calibration/[stuff2]_white.tifcalibration
ct-data/calibration/geopar.cfgcalibration
ct-data/proj_000_0_log.csvproj
ct-data/proj_000_0_00_[NNN].tifwhere NNN is the indexproj
Results/CT_[Scan]_80um.logNot maintaining folder structureCT_[Scan]_80um.loglogRECON
Results/CT_[Scan]_80um.niiNot maintaining folder structureCT_[Scan]_80um.niiNIFTIRECON

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.

Metadata

Instrument SourceLogicConfig SourceXNAT 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 ImagingAcquisition Site

Data

Original structureNoteXNAT structureXNAT 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]_stuffPET (Reconstructed)
D:\smis\dev\Data\[Subject ID]\Spectroscopy\[Series]\[Series]_0Spectroscopy\Session\[Series]\MRD, SPR
D:\smis\dev\MRD\[Subject ID]\Image\[Series]\[Series]_0MRD, RPR, rtv\Session\[Series]\MRD, RPR
D:\smis\dev\MRD\[Subject ID]\Image\[Series]\[Series]_0_oMRD, RPR, rtv\Session\[Series]\MRD, RPR
D:\smis\dev\MRD\[Subject ID]\Image\[Series]\btable.txtMRD, RPR, rtv\Session\[Series]\btable
D:\smis\dev\MRD\[Subject ID]\Image\[Series]\rtable.txtMRD, RPR, rtv\Session\[Series]\rtable
D:\smis\dev\PetRaw\[Subject ID]\[Series]\pet_[Series]PET (RAW)

3 - Siemens ARTIS pheno

Metadata

Instrument SourceLogicConfig SourceXNAT Destination
Additional Info field: Project:HT-003(0010,4000) Patient’s Comments(0010,4000) Patient’s CommentsProject: HT-003
Lastname:Mukherjee
Firstname:Sheep1
Title:
(0010,0010) Patient’s Name(0010,0010) Patient’s NameSubject: 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 UIDSCAN 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 structureNoteXNAT structure
[Path]//[File].jpgTo be covered with DICOM2JPEGResource file
[Path]//[File].aviResource file
[Path]//[File].txtResource file
[Path]//[File].csvResource file