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sct-pipeline / critical-ms-lesion

Detection of critical MS lesion in the spinal cord
GNU Lesser General Public License v2.1
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Curation of data received #1

Open plbenveniste opened 1 week ago

plbenveniste commented 1 week ago

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

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

jcohenadad commented 1 week ago

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 commented 2 days ago

As mentioned in https://github.com/sct-pipeline/critical-ms-lesion/issues/2#issue-2645064118, we only focus on focus on specific contrasts. Here is the code used to bidsify these specific volumes from DICOM to BIDS.

Code used ```bash # 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