Inquiry Regarding Availability of .nii.gz Demo Data of Lumbar

SCT
1

I am interested in conducting segmentation related to the lumbar region by SCT.
However, I could not find any open-source lumber data with .nii.gz format.

Could you kindly advise if such demo data is accessible?

Thank you very much for your time and assistance.

Sincerely,
Yuexiang Ji

2

Hi,

I am not aware of open-access lumbar data.

Note: if you wish to segment lumbar data, I invite you to try a lumbar spinal cord segmentation model from SCT. See the last one listed:

sct_deepseg -list-tasks

--
Spinal Cord Toolbox (git-master-76c27e16f13974de3ff8f81e25c92abe8f6d80ec)

sct_deepseg -list-tasks-long
--
TASK                          DESCRIPTION                                       CONTRAST       MODELS
------------------------------------------------------------------------------------------------------------------------
seg_sc_t2star                 Cord segmentation on T2*-weighted contrast        t2star         t2star_sc
seg_mice_sc                   Cord segmentation on mouse MRI                    t1             mice_uqueensland_sc
seg_mice_gm                   Gray matter segmentation on mouse MRI             t1             mice_uqueensland_gm
seg_tumor_t2                  Cord tumor segmentation on T2-weighted contrast   t2             findcord_tumor, t2_tumor
seg_ms_sc_mp2rage             Cord segmentation on MP2RAGE in MS patients       mp2rage        model_seg_ms_sc_mp2rage
seg_ms_lesion_mp2rage         MS lesion segmentation on cropped MP2RAGE data    mp2rage        model_seg_ms_lesion_mp2rage
seg_tumor-edema-cavity_t1-t2  Multiclass cord tumor/edema/cavity segmentation   t1, t2         findcord_tumor, model_seg_sctumor-edema-cavity_t2-t1_unet3d-multichannel
seg_exvivo_gm-wm_t2           Grey/white matter seg on exvivo human T2w         t2             model_seg_exvivo_gm-wm_t2_unet2d-multichannel-softseg
seg_gm_sc_7t_t2star           SC/GM seg on T2*-weighted contrast at 7T          t2star         model_7t_multiclass_gm_sc_unet2d
seg_lumbar_sc_t2w             Lumbar cord segmentation with 3D UNet             t2             model_seg_epfl_t2w_lumbar_sc

And for more details:

sct_deepseg -list-tasks-long
...
TASK:             seg_lumbar_sc_t2w
LONG_DESCRIPTION: This segmentation model for T2w spinal cord segmentation uses a 3D UNet architecture, and was created with the ivadomed package. Training data was
                  provided by Nawal Kinany and Dimitry Van De Ville of EPFL, with the files consisting of lumbar T2w scans (and manual spinal cord segmentations) of
                  11 healthy (non-pathological) patients.
URL:              https://github.com/ivadomed/lumbar_seg_EPFL
1 Like
3

Dear @jcohenadad

Thank you for your valuable guidance.
I will explore the lumber segmentation tool in SCT, as you have kindly suggested.

Sincerely,
Yuexiang Ji