neuropoly / data-management

Repo that deals with datalad aspects for internal use

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New dataset `exvivo-spinal-cord` #311

Closed Nilser3 closed 4 months ago

Nilser3 commented 4 months ago

Description

Dataset for managing ex-vivo human spinal cord MRI data. Potentially useful for training new GM/WM segmentation models. The idea is to add more subjects, for the moment 02 subjects to start with.

Details

sub-exvivo001

from Calabrese et al., (2018)
Modality: 7T GRE T2star, RD, MD, FA, DWI, B0, AD
Resolution: ${100 µm^3}$ isotropic
Levels: C1-L5
GT: GM and WM

sub-exvivo002

from Henmar et al., (2020)
Data available on : Link
Modality: 9.4T T2w RARE
Resolution: $50 x 50 x 200 µm ^3 $
Levels: C3-L5
GT: GM and WM

Nilser3 commented 4 months ago

Hi @mguaypaq, Could you please create a repository for exvivo-spinal-cord dataset Thank you

Nilser3 commented 4 months ago

Potential subject to add:

Currently on model_seg_exvivo_gm-wm_t2_unet2d-multichannel-softseg dataset there is a subject with top and bottom acquisitions, with incomplete segmentations (see images). This data was used to train seg_exvivo_gm-wm_t2

I propose to centralize this subject on exvivo-spinal-cord dataset, with a previous culmination/correction of its GM/WM segmentations.

Comments please @jcohenadad

jcohenadad commented 4 months ago

~also tagging @plbenveniste who worked on this~

EDIT Julien Cohen-Adad 2024-05-27: nevermind, I confused with the mouse exvivo dataset

mguaypaq commented 4 months ago

Done: I created the new repo here, and added @Nilser3 and @plbenveniste as collaborators (so that they have write access): https://data.neuro.polymtl.ca/datasets/exvivo-spinal-cord

For actually adding the data, you should open a pull request over there. You can see the instructions on the lab manual: https://intranet.neuro.polymtl.ca/data/git-datasets.html#making-a-pull-request