BIBSNet Outputs🔗
BIBSNet generates brain segmentations, brain masks, and ROI volumes in native T1w and/or T2w space (depending on the presence of T1w and/or T2w files in the input BIDS):
- Brain segmentation files in native T1w/T2w space
- Brain mask files in native T1w/T2w space
- Brain volumes computed for segmented ROIs in native T1w/T2w space
The derivative output folder is organized as follows. Note that each image file (.nii.gz) and .tsv is accompanied by a sidecar .json file that contains metadata for that file:
derivatives/
|_ bibsnet/
|_ sub-01/
|_ ses-A/
|_ anat/
|_ sub-01_ses-A_space-<T1w|T2w>_desc-aseg_dseg.nii.gz # Brain segmentation(s)
|_ sub-01_ses-A_space-<T1w|T2w>_desc-aseg_dseg.json
|_ sub-01_ses-A_space-<T1w|T2w>_desc-brain_mask.nii.gz # Brain mask(s)
|_ sub-01_ses-A_space-<T1w|T2w>_desc-brain_mask.json
|_ sub-01_ses-A_space-<T1w|T2w>_desc-aseg_volumes.tsv # Brain ROI volumes
|_ sub-01_ses-A_space-<T1w|T2w>_desc-aseg_volumes.json
Sidecar JSONs🔗
A sidecar JSON will be made for each of the .nii.gz files in derivatives.
Below is an example JSON for a file sub-01_ses-A_space-T1w_desc-aseg_dseg.json generated by BIBSnet version 3.0.0 and above
{
"Name": "BIBSnet Outputs",
"BIDSVersion": "1.4.0",
"DatasetType": "derivative",
"GeneratedBy": [
{
"Name": "BIBSnet",
"Version": "3.0.0",
"Container": {
"Type": "docker",
"Tag": "dcanumn/bibsnet:3.0.0"
}
}
],
"SpatialReference":"sub-01/ses-A/anat/sub-01_ses-A_T1w.nii.gz"
}
Working Directory🔗
├── work_dir/
├── prebibsnet/
| ├── sub-01/
| ├── ses-A/
| ├── averaged/
| | ├── <T1w|T2w>_denoise_and_bfcorrect/
| | | ├── clip/
| | | ├── denoise/
| | | ├── final_clip/
| | | ├── n4_correct/
| | | ├── d3.js
| | | ├──graph.json
| | | ├──graph1.json
| | | ├──index.html
| | ├── sub-150712_ses-V02_0000.nii.gz
| | ├── sub-150712_ses-V02_0001.nii.gz
| |
| ├── cropped/
| | ├── T1w/
| | | ├── brainmask.nii.gz
| | | ├── crop2full.mat
| | | ├── sub-01_ses-A_0000.nii.gz
| | ├── T2w/
| | ├── brainmask.nii.gz
| | ├── crop2full.mat
| | ├── sub-01_ses-A_0001.nii.gz
| |
| ├── resized/
| ├── ACPC_align/
| | ├── ACPC_T1w_registered_to_T1w.nii.gz
| | ├── ACPC_T2w_registered_to_T1w.nii.gz
| | ├── ACPC_aligned_<T1w|T2w>.nii.gz
| | ├── <T1w|T2w>_acpc2rigidbody.mat
| | ├── <T1w|T2w>_crop2acpc.mat
| | ├── <T1w|T2w>_full2acpc.mat
| | ├── <T1w|T2w>_full2crop.mat
| | ├── T2w_to_rigidbody.mat
| | ├── cropT2tocropT1.mat
| | ├── crop_<T1w|T2w>_to_BIBS_template.mat
| | ├── preBIBSnet_final_0000.nii.gz
| | ├── preBIBSnet_final_0001.nii.gz
| |
| ├── xfms/
| ├── <T1w|T2w>_to_BIBS.nii.gz
| ├── T2w_registered_to_T1w.nii.gz
| ├── cropT2tocropT1.mat
| ├── crop_<T1w|T2w>_to_BIBS_template.mat
| ├── full2crop<T1w|T2w>.mat
| ├── full2cropT2toT1.mat
| ├── full_crop_<T1w|T2w>_to_BIBS_template.mat
| ├── preBIBSnet_final_0000.nii.gz
| ├── preBIBSnet_final_0001.nii.gz
|
├── bibsnet/
| ├── sub-01/
| ├── ses-A/
| ├── input/
| | ├── sub-01_ses-A_optimal_resized_0000.nii.gz
| | ├── sub-01_ses-A_optimal_resized_0001.nii.gz
| ├── output/
| ├── plans.pkl
| ├── prediction_time.txt
| ├── sub-01_ses-A_optimal_resized.nii.gz
|
├── postbibsnet/
├── sub-01/
├── ses-A/
├── preBIBSnet_full_crop_T1w_to_BIBS_template.mat
├── preBIBSnet_full_crop_T2w_to_BIBS_template.mat
├── seg_reg_to_T1w_native.mat
├── seg_reg_to_T2w_native.mat