New dataset lumbar-marseille

[valosekj]

I would like to push a new dataset marseille-lumbar to our git-annex server.

@mguaypaq or @nullnik-0, can you please initialize the dataset and give me r/w permissions? Thanks!

[mguaypaq]

I'm going to name it lumbar-marseille instead, to match our other lumbar datasets.

[mguaypaq]

I created the repo and gave @valosekj write access:
https://data.neuro.polymtl.ca/datasets/lumbar-marseille

[valosekj]

I'm working on the BIDSification.

input folder

sub-CTS04_ses-SPpre_Localizer_3sag.nii
sub-CTS04_ses-SPpre_T2w.nii.gz
sub-CTS04_ses-SPpre_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS04_ses-SPpre_acq-zoomit_T2w.nii.gz
sub-CTS05_ses-SPpre_Localizer_3sag.nii
sub-CTS05_ses-SPpre_T2w.nii.gz
sub-CTS05_ses-SPpre_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS05_ses-SPpre_acq-zoomit_T2w.nii.gz
sub-CTS10_ses-SPanat_Localizer_3sag.nii
sub-CTS10_ses-SPanat_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS10_ses-SPanat_acq-zoomit_T2w.nii.gz
sub-CTS14_ses-SPpre_Localizer_3sag.nii
sub-CTS14_ses-SPpre_T2w.nii.gz
sub-CTS14_ses-SPpre_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS14_ses-SPpre_acq-zoomit_T2w.nii.gz
sub-CTS15_ses-SPpre_Localizer_3sag.nii
sub-CTS15_ses-SPpre_T2w.nii.gz
sub-CTS15_ses-SPpre_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS15_ses-SPpre_acq-zoomit_T2w.nii.gz
sub-CTS20_ses-SPpre_Localizer_3sag.nii
sub-CTS20_ses-SPpre_T2w.nii.gz
sub-CTS20_ses-SPpre_T2w_rootlets_resampled_inzoomit.nii.gz
sub-CTS20_ses-SPpre_acq-zoomit_T2w.nii.gz

output BIDS folder

valosek@macbook-pro:~/data/data.neuro.polymtl.ca/lumbar-marseille$ tree                                                                                                                                                                                                                                                                                       (master|-1…2)
.
├── README.md
├── code
│   ├── curate.py
│   └── curate.sh
├── dataset_description.json
├── derivatives
│   └── labels
│       ├── sub-CTS04
│       │   └── ses-SPpre
│       │       └── anat
│       │           ├── sub-CTS04_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.json
│       │           └── sub-CTS04_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz
│       ├── sub-CTS05
│       │   └── ses-SPpre
│       │       └── anat
│       │           ├── sub-CTS05_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.json
│       │           └── sub-CTS05_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz
│       ├── sub-CTS10
│       │   └── ses-SPanat
│       │       └── anat
│       │           ├── sub-CTS10_ses-SPanat_acq-ax_T2w_label-rootlets_dseg.json
│       │           └── sub-CTS10_ses-SPanat_acq-ax_T2w_label-rootlets_dseg.nii.gz
│       ├── sub-CTS14
│       │   └── ses-SPpre
│       │       └── anat
│       │           ├── sub-CTS14_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.json
│       │           └── sub-CTS14_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz
│       ├── sub-CTS15
│       │   └── ses-SPpre
│       │       └── anat
│       │           ├── sub-CTS15_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.json
│       │           └── sub-CTS15_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz
│       └── sub-CTS20
│           └── ses-SPpre
│               └── anat
│                   ├── sub-CTS20_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.json
│                   └── sub-CTS20_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz
├── participants.json
├── participants.tsv
├── sub-CTS04
│   └── ses-SPpre
│       └── anat
│           ├── sub-CTS04_ses-SPpre_acq-ax_T2w.nii.gz
│           ├── sub-CTS04_ses-SPpre_acq-localizer.nii.gz
│           └── sub-CTS04_ses-SPpre_acq-sag_T2w.nii.gz
├── sub-CTS05
│   └── ses-SPpre
│       └── anat
│           ├── sub-CTS05_ses-SPpre_acq-ax_T2w.nii.gz
│           ├── sub-CTS05_ses-SPpre_acq-localizer.nii.gz
│           └── sub-CTS05_ses-SPpre_acq-sag_T2w.nii.gz
├── sub-CTS10
│   └── ses-SPanat
│       └── anat
│           ├── sub-CTS10_ses-SPanat_acq-ax_T2w.nii.gz
│           └── sub-CTS10_ses-SPanat_acq-localizer.nii.gz
├── sub-CTS14
│   └── ses-SPpre
│       └── anat
│           ├── sub-CTS14_ses-SPpre_acq-ax_T2w.nii.gz
│           ├── sub-CTS14_ses-SPpre_acq-localizer.nii.gz
│           └── sub-CTS14_ses-SPpre_acq-sag_T2w.nii.gz
├── sub-CTS15
│   └── ses-SPpre
│       └── anat
│           ├── sub-CTS15_ses-SPpre_acq-ax_T2w.nii.gz
│           ├── sub-CTS15_ses-SPpre_acq-localizer.nii.gz
│           └── sub-CTS15_ses-SPpre_acq-sag_T2w.nii.gz
└── sub-CTS20
    └── ses-SPpre
        └── anat
            ├── sub-CTS20_ses-SPpre_acq-ax_T2w.nii.gz
            ├── sub-CTS20_ses-SPpre_acq-localizer.nii.gz
            └── sub-CTS20_ses-SPpre_acq-sag_T2w.nii.gz

`acq-ax_T2w_label-rootlets_dseg.json` contains the following:

{
    "SpatialReference": "orig",
    "GeneratedBy": [
        {
            "Name": "Manual",
            "Author": "Raphaëlle Schlienger",
            "Date": "2024-05-22"
        }
        {
            "Name": "flirt",
            "Author": "Jan Valosek",
            "Date": "2024-05-24"
            "Note": "The rootlets were segmented on the resampled image. Thus I used flirt to resample rootlets back to the native space. Context: https://github.com/ivadomed/model-spinal-rootlets/issues/46"
        }
    ]
}

@jcohenadad, @NathanMolinier, any suggestions or comments?

[NathanMolinier]

The suffix is missing in your localizer names. You should add the contrast at the end.

sub-CTS20_ses-SPpre_acq-localizer.nii.gz --> sub-CTS20_ses-SPpre_acq-localizer_T?w.nii.gz

Do you have more information about the contrast used ?

[valosekj]

The suffix is missing in your localizer names. You should add the contrast at the end.

sub-CTS20_ses-SPpre_acq-localizer.nii.gz --> sub-CTS20_ses-SPpre_acq-localizer_T?w.nii.gz

Do you have more information about the contrast used ?

good catch! but, it is not easy to say which contrast the localizer is. it seems to be some dynamic-based sequence to be acquired fast (nor purely T1w or T2w)

So maybe we can use localizer as the suffix: sub-CTS20_ses-SPpre_localizer.nii.gz

[jcohenadad]

Question about localizer posted on the BIDS forum

[valosekj]

The first version of the dataset is pushed now! Details in this issue. I will update the localizer naming afterwards.

To download the data:

git clone [email protected]:datasets/lumbar-marseille
cd lumbar-marseille
git annex dead here
git checkout jv/add_6subjects
git annex get .

Example command to open one subject using FSLeyes:

fsleyes sub-CTS04/ses-SPpre/anat/sub-CTS04_ses-SPpre_acq-localizer.nii.gz sub-CTS04/ses-SPpre/anat/sub-CTS04_ses-SPpre_acq-ax_T2w.nii.gz sub-CTS04/ses-SPpre/anat/sub-CTS04_ses-SPpre_acq-sag_T2w.nii.gz derivatives/labels/sub-CTS04/ses-SPpre/anat/sub-CTS04_ses-SPpre_acq-ax_T2w_label-rootlets_dseg.nii.gz -cm random -dr 19 28

[valosekj]

Question about localizer posted on the BIDS forum

Okay. The answer on the forum suggests anat/<entities>_acq-scout_T1w.nii.gz. This is similar to the suggestion from @NathanMolinier. However, we do not know the contrast (T1w or T2w)...

[jcohenadad]

it’s usually a short TR and very short TE (few ms) so i’d say T1

[valosekj]

it’s usually a short TR and very short TE (few ms) so i’d say T1

Okay! _T1w suffix added in https://data.neuro.polymtl.ca/datasets/lumbar-marseille/commit/a5bb75dc8d43c2d21e7407c88f4efd389c2db49c.