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Merge pull request #9 from alexpron/heudiconv
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[ENH]: DICOM to NIFTI BIDS conversion with Heudiconv
@quentinduche
quentinduche authored Jul 25, 2024
2 parents 32f4b73 + d98a8bb commit f4370b5
Showing 5 changed files with 855 additions and 416 deletions.
45 changes: 32 additions & 13 deletions README.md
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@@ -29,14 +29,20 @@ conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK b
```
## Usage

There are three scripts to download datasets:
- `shanoir_downloader.py` simply downloads datasets from a id, a list of ids, or directly from a [shanoir search as on the shanoir solr search page](https://shanoir.irisa.fr/shanoir-ng/solr-search),
- `shanoir_downloader_check.py` is a more complete tool ; it enables to download datasets (from a csv or excel file containing a list of dataset ids, or directly from a [shanoir search as on the shanoir solr search page](https://shanoir.irisa.fr/shanoir-ng/solr-search)), verify their content, anonymize them and / or encrypt them.
- `shanoir2bids.py` uses `shanoir_downloader.py` to download Shanoir datasets and reorganises them into a BIDS data structure that is specified by the user with a `.json` configuration file. An example of configuration file is provided `s2b_example_config.json`.
## How to download Shanoir datasets ?

`shanoir_downloader_check.py` creates two files in the output folder:
- `downloaded_datasets.csv` records the successfully downloaded datasets,
- `missing_datasets.csv` records the datasets which could not be downloaded.
There are three scripts to download datasets from a Shanoir instance:

1.`shanoir_downloader.py`: downloads datasets from a id, a list of ids, or directly from a [shanoir search as on the shanoir solr search page](https://shanoir.irisa.fr/shanoir-ng/solr-search),

2.`shanoir_downloader_check.py`: a more complete tool ; it enables to download datasets (from a csv or excel file containing a list of dataset ids, or directly from a [shanoir search as on the shanoir solr search page](https://shanoir.irisa.fr/shanoir-ng/solr-search)), verify their content, anonymize them and / or encrypt them.

3.`shanoir2bids.py`: Download datasets from Shanoir in DICOM format and convert them into datalad datasets in BIDS format. The conversion is parameterised by a configuration file in `.json` format.

### `shanoir_downloader_check.py`
- `shanoir_downloader_check.py` creates two files in the output folder:
- `downloaded_datasets.csv` records the successfully downloaded datasets,
- `missing_datasets.csv` records the datasets which could not be downloaded.

With those two files, `shanoir_downloader_check.py` is able to resume a download session (the downloading can be interrupted any time, the tool will not redownload datasets which have already been downloaded).

@@ -50,7 +56,11 @@ See `python shanoir_downloader_check.py --help` for more information.

You might want to skip the anonymization process and the encryption process with the `--skip_anonymization` and `--skip_encryption` arguments respectively (or `-sa` and `-se`).

For `shanoir2bids.py`, a configuration file must be provided to transform a Shanoir dataset into a BIDS dataset.

### `shanoir2bids.py`

A `.json` configuration file must be provided to transform a Shanoir dataset into a BIDS dataset.

```
-----------------------------[.json configuration file information]-------------------------------
This file will tell the script what Shanoir datasets should be downloaded and how the data will be organised.
@@ -61,31 +71,40 @@ The dictionary in the json file must have four keys :
"data_to_bids": list of dict, each dictionary specifies datasets to download and BIDS format with the following keys :
-> "datasetName": str, Shanoir name for the sequence to search
-> "bidsDir" : str, BIDS subdirectory sequence name (eg : "anat", "func" or "dwi", ...)
-> "bidsName" : str, BIDS sequence name (eg: "t1w-mprage", "t2-hr", "cusp66-ap-b0", ...)
-> "bidsName" : str, BIDS sequence name (eg: "t1w", "acq-b0_dir-AP", ...)
```
Please refer to the [BIDS starter kit](https://bids-standard.github.io/bids-starter-kit/folders_and_files/files.html)
for exhaustive templates of filenames. A BIDS compatible example is provided in the file `s2b_example_config.json`.

An example is provided in the file `s2b_example_config.json`.

To download longitudinal data, a key `session` and a new entry `bidsSession` in `data_to_bids` dictionaries should be defined in the JSON configuration files. Of note, only one session can be downloaded at once. Then, the key `session` is just a string, not a list as for subjects.


### Example usage

### Download Examples
#### Raw download

To download datasets, verify the content of them, anonymize them and / or encrypt them you can use a command like:

`python shanoir_downloader_check.py -u username -d shanoir.irisa.fr -ids path/to/datasets_to_download.csv -of path/to/output/folder/ -se -lf path/to/downloads.log`

The `example_input_check.csv` file in this repository is an example input file (the format of the `datasets_to_download.csv` file should be the same).


#### Solr search download

You can also download datasets from a [SolR search](https://shanoir.irisa.fr/shanoir-ng/solr-search) as on the website:

`python shanoir_downloader.py -u amasson -d shanoir.irisa.fr -of /data/amasson/test/shanoir_test4 --search_text "FLAIR" -p 1 -s 2 `

where `--search_text` is the string you would use on [the SolR search page](https://shanoir.irisa.fr/shanoir-ng/solr-search) (for example `(subjectName:(CT* OR demo*) AND studyName:etude test) OR datasetName:*flair*`). More information on the info box of the SolR search page.

`python shanoir2bids.py -c s2b_example_config.json -d my_download_dir` will download Shanoir files identified in the configuration file and saves them as a BIDS data structure into `my_download_dir`
#### BIDS download
`python shanoir2bids.py -j s2b_example_config.json -of my_download_dir --outformat nifti` will download Shanoir datasets identified in the configuration file saves them as DICOM and convert them into a BIDS datalad dataset into `my_download_dir`.

## About Solr Search

### Search usage

The `--search_text` and `--expert_mode` arguments work as on the [Shanoir search page](https://shanoir.irisa.fr/shanoir-ng/solr-search).

8 changes: 7 additions & 1 deletion pyproject.toml
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@@ -23,7 +23,13 @@ readme = "README.md"
license = {file = "LICENSE"}
keywords = ["Shanoir", "DICOM", "NIFTI", "BIDS"]
classifiers = [
"Programming Language :: Python"

"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10"

]

[project.urls]
36 changes: 23 additions & 13 deletions s2b_example_config.json
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@@ -1,19 +1,29 @@
{
"study_name": "Aneravimm",
"subjects": ["VS_Aneravimm_010", "VS_Aneravimm_011"],
"data_to_bids":
[
{"datasetName": "t1_mprage_sag_p2_iso", "bidsDir": "anat", "bidsName": "acq-mprage_T1w"},
"study_name": "Aneravimm",
"subjects": ["VS_Aneravimm_010", "VS_Aneravimm_011"],
"data_to_bids": [
{"datasetName": "t1_mprage_sag_p2_iso", "bidsDir": "anat", "bidsName": "acq-mprage_T1w"},
{"datasetName": "t2_tse_HR_cor_MTL", "bidsDir": "anat", "bidsName": "acq-hr_T2w"},
{"datasetName": "Resting State_bold AP 1.6mm HIPP", "bidsDir": "func", "bidsName": "task-restingState_acq-hipp_dir-AP_bold"},
{"datasetName": "Resting State_bold AP 1.6mm HIPP", "bidsDir": "func", "bidsName": "task-restingState_dir-AP_bold"},
{"datasetName": "Diff cusp66 b3000 AP 1.5mm", "bidsDir": "dwi", "bidsName": "acq-b3000_dir-AP_dwi"},
{"datasetName": "Diff cusp66 b0 PA 1.5mm", "bidsDir": "dwi", "bidsName": "acq-b0_dir-AP_dwi"},
{"datasetName": "Diff cusp66 b0 PA 1.5mm", "bidsDir": "dwi", "bidsName": "acq-b0_dir-PA_dwi"}
],
"dcm2niix":"/home/qduche/Software/dcm2niix_lnx/dcm2niix",
"dcm2niix_options": "-v 0 -z y",
"find_and_replace_subject":
[
{"find":"VS_Aneravimm_", "replace": "VS"},
{"find":"Vs_Aneravimm_", "replace": "VS"}
]
"dcm2niix": "/home/alpron/softs/miniconda3/envs/test-env/bin/dcm2niix",
"dcm2niix_options_comment": "dcm2niix configuration options in the nipype format (see https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.dcm2nii.html)",
"dcm2niix_options": {
"bids_format": true,
"anon_bids": true,
"compress": "y",
"compression": 5,
"crop": false,
"has_private": false,
"ignore_deriv": false,
"single_file": false,
"verbose": false
},
"find_and_replace_subject": [
{"find": "VS_Aneravimm_", "replace": "VS"},
{"find": "Vs_Aneravimm_", "replace": "VS"}
]
}
374 changes: 306 additions & 68 deletions s2b_example_config_EMISEP_long.json
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@@ -1,70 +1,308 @@
{
"study_name": "EMISEP",
"subjects": ["08-74"],
"session": "08-74 MO ENCEPHALE",
"data_to_bids":
[
{"datasetName": "3D T1 MPRAGE", "bidsDir": "brain", "bidsName": "t1w", "bidsSession": "M00"},
{"datasetName": "*3d flair*", "bidsDir": "brain", "bidsName": "flair", "bidsSession": "M00"},
{"datasetName": "*c1c3*", "bidsDir": "spinalCord", "bidsName": "t2ax_C1C3", "bidsSession": "M00"},
{"datasetName": "*c1-c3*", "bidsDir": "spinalCord", "bidsName": "t2ax_C1C3", "bidsSession": "M00"},

{"datasetName": "*c4c7*", "bidsDir": "spinalCord", "bidsName": "t2ax_C4C7", "bidsSession": "M00"},
{"datasetName": "*c4-c7*", "bidsDir": "spinalCord", "bidsName": "t2ax_C4C7", "bidsSession": "M00"},


{"datasetName": "t2_tse_rr_p2_sag", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "t2_tse_rr_p2_sag2.5 te 81", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_384", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_p2", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "SAG T2 CERV", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},
{"datasetName": "SAG T2 DORSAL", "bidsDir": "spinalCord", "bidsName": "t2Sag", "bidsSession": "M00"},

{"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp_sp", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "t2_tse_rr_p2_sag_comp_sp", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_384_comp_sp", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260_comp_ad", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "t2_tse_sag_p2_comp_ad", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},
{"datasetName": "SAG T2 TSE MOELLE", "bidsDir": "spinalCord", "bidsName": "t2Sag-COMP", "bidsSession": "M00"},



{"datasetName": "t1_fl3d_sag_p2_iso", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_sag_p2_iso mt", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_tra_p2_iso", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_tra_p2_iso mt", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso mt_tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso tr38", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt sans sat", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat_mt", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38_sans_sat", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_iso_tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_m0_iso tr38 sans sat", "bidsDir": "spinalCord", "bidsName": "mt0", "bidsSession": "M00"},
{"datasetName": "t1_fl3d_we_tra_p2_mt_iso tr38", "bidsDir": "spinalCord", "bidsName": "mt1", "bidsSession": "M00"},


{"datasetName": "3d_t1_mprage_sag", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso cerv", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso cerv_rr", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso ofsep", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_axial", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_cor", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_tra", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "t1_mprage_sag_p2_iso ofsep_rr", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"},
{"datasetName": "T1 MPRAGE CERV", "bidsDir": "spinalCord", "bidsName": "t1Sag", "bidsSession": "M00"}

],
"dcm2niix":"/home/mgaubert/Software/dcm2niix/dcm2niix_v1.0.20211006/dcm2niix",
"dcm2niix_options": "-v 0 -z y -ba n"
"study_name": "EMISEP",
"subjects": ["08-74"],
"session": "08-74 MO ENCEPHALE",
"data_to_bids": [
{
"datasetName": "3D T1 MPRAGE",
"bidsDir": "brain",
"bidsName": "T1w",
"bidsSession": "M00"
},
{
"datasetName": "*3d flair*",
"bidsDir": "brain",
"bidsName": "FLAIR",
"bidsSession": "M00"
},
{
"datasetName": "*c1c3*",
"bidsDir": "spinalCord",
"bidsName": "t2ax_C1C3",
"bidsSession": "M00"
},
{
"datasetName": "*c1-c3*",
"bidsDir": "spinalCord",
"bidsName": "t2ax_C1C3",
"bidsSession": "M00"
},
{
"datasetName": "*c4c7*",
"bidsDir": "spinalCord",
"bidsName": "t2ax_C4C7",
"bidsSession": "M00"
},
{
"datasetName": "*c4-c7*",
"bidsDir": "spinalCord",
"bidsName": "t2ax_C4C7",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_rr_p2_sag",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_rr_p2_sag2.5 te 81",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_384",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_p2",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "SAG T2 CERV",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "SAG T2 DORSAL",
"bidsDir": "spinalCord",
"bidsName": "t2Sag",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp_sp",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_rr_p2_sag_comp_sp",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_384_comp_sp",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260_comp_ad",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t2_tse_sag_p2_comp_ad",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "SAG T2 TSE MOELLE",
"bidsDir": "spinalCord",
"bidsName": "t2Sag-COMP",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_sag_p2_iso",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_sag_p2_iso mt",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_tra_p2_iso",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_tra_p2_iso mt",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso mt_tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso tr38",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat_mt",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38_sans_sat",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_iso_tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_m0_iso tr38 sans sat",
"bidsDir": "spinalCord",
"bidsName": "mt0",
"bidsSession": "M00"
},
{
"datasetName": "t1_fl3d_we_tra_p2_mt_iso tr38",
"bidsDir": "spinalCord",
"bidsName": "mt1",
"bidsSession": "M00"
},
{
"datasetName": "3d_t1_mprage_sag",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso cerv",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso cerv_rr",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso ofsep",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_axial",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_cor",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_tra",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "t1_mprage_sag_p2_iso ofsep_rr",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
},
{
"datasetName": "T1 MPRAGE CERV",
"bidsDir": "spinalCord",
"bidsName": "t1Sag",
"bidsSession": "M00"
}
],
"dcm2niix": "~/softs/miniconda3/bin/dcm2niix",
"dcm2niix_options_comment": "dcm2niix configuration options in the nipype format (see https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.dcm2nii.html)",
"dcm2niix_options": {
"bids_format": true,
"anon_bids": true,
"compress": "y",
"compression": 5,
"crop": false,
"has_private": false,
"ignore_deriv": false,
"single_file": false,
"verbose": true
}
}


808 changes: 487 additions & 321 deletions shanoir2bids.py
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