Open Nilser3 opened 4 months ago
i think "desc-rater1" should not go at the end @NathanMolinier can confirm
i think "desc-rater1" should not go at the end @NathanMolinier can confirm
Yes, it should not indeed. Also, the suffix _seg
is missing (or _dseg
if multiple types of lesions are segmented).
See the corrected tree below for marseille-3T-mp2rage
:
├── derivatives
│ └── labels
│ ├── sub-MRS00
│ │ └── ses-M0
│ │ └── anat
│ │ ├── sub-MRS00_ses-M0_UNIT1_desc-rater1_label-lesion_seg.json
│ │ ├── sub-MRS00_ses-M0_UNIT1_desc-rater1_label-lesion_seg.nii.gz
│ │ ├── sub-MRS00_ses-M0_UNIT1_desc-rater2_label-lesion_seg.json
│ │ ├── sub-MRS00_ses-M0_UNIT1_desc-rater2_label-lesion_seg.nii.gz
There is also a problem here with the basel-mp2rage
dataset:
├── derivatives
│ └── labels
│ ├── sub-C001
│ │ └── anat
│ │ ├── sub-C001_UNIT1_label-SC_seg.json
│ │ └── sub-C001_UNIT1_label-SC_seg.nii.gz
...
│ ├── sub-P001
│ │ └── anat
│ │ ├── sub-P001_UNIT1_label-SC_seg.json
│ │ ├── sub-P001_UNIT1_label-SC_seg.nii.gz
│ │ ├── sub-P001_UNIT1_desc-rater1_label-lesion_seg.json <-----------
│ │ ├── sub-P001_UNIT1_desc-rater1_label-lesion_seg.nii.gz <-----------
│ │ ├── sub-P001_UNIT1_desc-rater2_label-lesion_seg.json <-----------
│ │ ├── sub-P001_UNIT1_desc-rater2_label-lesion_seg.nii.gz <-----------
│ │ ├── sub-P001_UNIT1_desc-rater3_label-lesion_seg.json <-----------
│ │ └── sub-P001_UNIT1_desc-rater3_label-lesion_seg.nii.gz <-----------
The name of the rater should be added instead to the .json
sidecar.
Thanks you @NathanMolinier
Following the new conventions, here is the modifications for basel-mp2rage
I have no details to fill in the JSON files for Haris nor Katrin segmentations:
Previous JSON sidecar : sub-P001_UNIT1_lesion-manualHaris.json
{
"Authors": [
"USB",
"Nilser Laines Medina"
],
"Label": "lesion-manual"
}
New JSON sidecar : sub-P001_UNIT1_desc-rater1_label-lesion_seg.json
{
"SpatialReference": "orig",
"GeneratedBy": [
{
"Name": "Manual",
"Author": "Haris",
"Date": ""
}
]
}
Previous JSON sidecar : sub-P001_UNIT1_lesion-manualNeuroPolyjson
{
"SpatialReference": "orig",
"GeneratedBy": [
{
"Name": "Manual",
"Author": "Katrin",
"Date": ""
}
]
}
New JSON sidecar : sub-P001_UNIT1_desc-rater3_label-lesion_seg.json
{
"SpatialReference": "orig",
"GeneratedBy": [
{
"Name": "Manual",
"Author": "Katrin",
"Date": ""
}
{
"Name": "Manual",
"Author": "Michelle Chen",
"Date": "2023-01-23"
}
]
}
Feedback please @mguaypaq
branch
: nlm/update_gt_names
commit
: 0177d5dcbfb15cd1ba808c7671b8b8a6de675901
Regarding the format for JSON sidecars, please check our intranet.
These are the fields which are needed:
{
"SpatialReference": "orig",
"GeneratedBy": [
{
"Name": "Manual",
"Author": "Nathan Molinier",
"Date": "2023-07-14 13:43:10"
}
]
}
Update for dataset: marseille-3T-mp2rage
branch
: nlm/update_gt_names
commit
: afd8282a1ee8d468fd4ab8769e82d4ffdd7acb67
Regarding the format for JSON sidecars, please check our intranet.
Thanks you @NathanMolinier , I have updated the JSON sidecars
For basel-mp2rage
: some of the json sidecars were missing a comma, so I added a commit to fix this, and merged into master
.
For marseille-3T-mp2rage
: some of the json sidecars had a extra commas, so I added a commit to fix this, and merged into master
.
For nih-ms-mp2rage
: I don't see any branches to merge on the server. @Nilser3, did you push your changes to this repo?
Oh, my bad, Thanks you @mguaypaq
For nih-ms-mp2rage
we don't have masks yet (so nothing to modify), but as soon as we have them I will send them to the git-annex respecting these new conventions.
Description
This issue will be used to update the GT segmentation names to be in conformity with the new conventions.
Current arborescence of datasets:
Data MP2RAGE
tree
basel-mp2rage
tree
marseille-3T-mp2rage
tree
nih-ms-mp2rage