Home

Welcome to the sct_testing_management wiki!

Convention for folder/file names

  |- center_study_subject
      info.dcm --> single dicom file (e.g. could be from the localizer) which includes useful info in the header, such as scanner type, model, subject demographics, center, etc.
      subject.txt --> csv formatted as follows: pathology=XX,
      |- t1
        |- t1.nii.gz
        |- t1_seg_manual.nii.gz
      |- t2
        |- t2.nii.gz
        |- t2_seg_manual.nii.gz
        |- t2_labels_disc_manual.nii.gz
      |- t2s
        |- t2s.nii.gz
        |- t2s_seg_manual.nii.gz
        |- t2s_gmseg_manual.nii.gz
      |- mt --> note that if a sequence has the suffix "_reg", it means that it is inherently registered with the sequence without "_reg", and hence the ground truth segmentation can be used for all contrasts within this folder
        |- mt1.nii.gz (or mt1_reg.nii.gz)
        |- mt0.nii.gz (or mt0_reg.nii.gz)
        |- t1w.nii.gz
        |- t1w_seg_manual.nii.gz
      |- dmri
        |- dwi_moco_mean.nii.gz
        |- dwi_moco_mean_seg_manual.nii.gz
        |- b0_moco_mean.nii.gz --> inherently registered with dwi_moco_mean.nii.gz, hence dwi_moco_mean_seg_manual.nii.gz can be used as ground truth segmentation

Convention for contrasts

• t1: Cord bright, CSF dark. Example of file names: t1/t1.nii.gz. Example images
• t2: Cord dark, CSF bright. Example of file names: t2/t2.nii.gz, dmri/b0_moco_mean.nii.gz. Example images
• t2s: Cord dark, CSF bright, Grey matter visible. Example of file names: mt/mt1, mt/mt0, gre, t2s. Example images
• dwi: Diffusion-weighted imaging. Cord bright, no other tissue visible. Example of file names: dmri/dwi_moco_mean.nii.gz. Example images

How to compress from .nii to .nii.gz

gzip -f FILENAME

If you are converting using dcm2niix, here is the thing to do to get nii.gz:

 dcm2niix -z