Curation of data received

[plbenveniste]

A first batch of data was received yesterday. It is only a sample to start creating the pipeline. It is in the DICOM format.

• Should this data be git-annexed ?
• If so, which git-annex dataset ?

This issue will also be used to describe the contrasts contained in the batch of data received.

[jcohenadad]

Should this data be git-annexed ?

usually, we would not do it for only one subject, too much trouble. On the other hand, anticipating that we will receive more data from this site (approx 90 patients), maybe it is in fact a good idea to create a git-annex entry for this dataset.

[plbenveniste]

As mentioned in #2 (comment), we only focus on focus on specific contrasts. Here is the code used to bidsify these specific volumes from DICOM to BIDS.

Code used

# For Csp Ax T2
dcm2niix -f 'sub-HC001_acq-axCerv_T2w' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/Csp_Ax_T2-20220509

# For Csp Sag 3D Fiesta
dcm2niix -f 'sub-HC001_acq-sagCerv_FIESTA' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/Csp_Sag_3D_Fiesta-20220509

# For Csp Sag Cube T2 Focus
dcm2niix -f 'sub-HC001_acq-sagCervCube_T2w' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/Csp_Sag_Cube_T2_Focus-20220509   

# For ORIG SAG T2 LOC UPPER DL
dcm2niix -f 'sub-HC001_acq-sagUpperLocalizer_T2w' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/ORIG_SAG_T2_LOC_UPPER_DL-20220509

# For Denoised SAG T2 LOC UPPER DL
dcm2niix -f 'sub-HC001_acq-sagUpperLocalizerDen_T2w' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/ORIG_SAG_T2_LOC_UPPER_DL-20220509

# For Csp Sag T2 STIR (only Csp)
dcm2niix -f 'sub-HC001_acq-sagCerv_STIR' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/ORIG_Csp_Sag_T2_STIR-20220509

# For Csp Ax MERGE (only Csp)
dcm2niix -f 'sub-HC001_acq-axCerv_MERGE' -o ms-mayo-bids/sub-HC001/anat -z y Anonymous_71e0421d-a61cfbc81cf9c8bbb0605733d6c68c5b1338b367/MR_INNOVATION-20220509/Csp_Ax_MERGE-20220509 

The data was moved to duke/temp/plben/ms-critical-lesion/ms-mayo-bids