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Dimitri Papadopoulos Orfanos edited this page Jan 31, 2019 · 20 revisions

We discuss software infrastructure for acquisition of MRI data in the c-VEDA project.

Workflow summary

Acquisition centres send a single imaging dataset per subject. A dataset shall be uploaded as a ZIP file containing folders, each folder containing a single sequence in the form of anonymized DICOM files. Detailed instructions for operators are collected in a Standard Operating Procedure (SOP) document.

MRI sequences

Acquisition centres will run the following MRI sequences during a single neuroimaging session. Depending on the acquisition centre, the databank team expect specific sequence names in the (0008,103E) Series Description DICOM tag:

Sequence Folder name PGIMER KOLKATA MYSORE NIMHANS (Siemens) NIMHANS (Philips)
1 Scout image —
2 Site specific calibration scans, if necessary —
3 3D T1 weighted volume T1w 3DT1 weighted volume MPRAGE T1W_IR_TSE 3D T1 WEIGHTED VOLUME
t1_mprage_sag 		3D T1 WEIGHTED VOLUME
4 Resting state fMRI rest Resting state fMRI ep2d_bold_moco_fmri FE_EPI 160 act_RESTINGSTATE fMRI
bas_Resting STATE fMRI 		RESTING STATE fMRI
5 B0 mapping, if available B0_map B0 mapping gre_field_mapping B0 mapping B0MAPPING
B 0 MAPPING
B 0 _mapping_2mm 		B0 MAPPING
6 DTI dwi DTI ep2d_diff_mddw_30_P>>A_p2_DFC_MIX DTI_high_32 DTI_DFC
DTI_DFC_MIX
DTI _30_DFC 		DTI
7 DTI - reversed dwi_rev DTI-reversed ep2d_diff_mddw_6_rev_A>>P_p2 DTI_6 DTI REVERSED_DFC
DTI REVERSED_DFC_MIX
DTI _6_DFC 		DTI REVERSED
DTI (A>>P phase encoding)✳ dwi_ap DTI 20 A>>P_DFC_MIX
DTI 20 A>>P_DFC
DTI 32 A>>P FOLLOW UP_DFC_MIX
DTI A>>P_DFC_MIX
DTI 32 A>>P FOLLOW UP_DFC
DTI 20 A>>P_DFC
8 2D fast FLAIR FLAIR 2D T2 weighted t2_tse_tra_p2 FLAIR 2D FASTFLAIR
2D FLAIR 		2D FAST FLAIR
9 2D T2 weighted T2w 2D fast FLAIR t2_tirm_tra_dark-fluid_fast_p2 T2W_TSE 2D T2 WEIGHTED
2D T2 TSE 		2D T2 WEIGHTED

✳ MRI sequence added at follow-up 1 in NIMHANS to mitigate the effect of disparate P>>A and A>>P phase encodings at baseline.

DICOM files from the imaging sessions are packed in a ZIP file. The structure of the ZIP file shall be as follows:

120003456789.zip
├── T1w
├── rest
├── B0_map
├── dwi
├── dwi_rev
├── dwi_ap
├── FLAIR
└── T2w

Anoymization

Acquisition centres use DicomEditor to anonymize neuroimaging data. Data sent to the databank identify subjects by their PSC1 code only. Depending on the acquisition site, the databank team expect the PSC1 code in specific DICOM tags:

ID Acquisition centre DICOM tag for PSC1 code
11 PGIMER (0010,0020) Patient ID
13 KOLKATA (0010,0010) Patient Name
15 MYSORE (0040,0280) Comments on the Performed Procedure Step
16 NIMHANS (Siemens) (0010,4000) Patient Comments
(0032, 4000) Study Comments (single acquisition after RIS)
(0010,0020) Patient ID (before RIS)
16 NIMHANS (Philips) (0032,4000) Study Comments

c-VEDA web site

c-VEDA database

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