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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