About the application
BIDS'em ALL is a java software that allows you to convert a folder containing raw DICOM data to niftis files automatically sorted according to the BIDS structure.
It uses a 6 steps procedure
- (1) Analyze all dicoms to extract patient and series data
- (2) Prompt the user to select the ID to use for the patients (it will be used for the BIDS "sub-XXX"). Per default, patient ID is used
- (3) For each serie that was not previously setup, it prompts the user to identify the datatype (T1w, FLAIR ...) of the serie identified by the key "ProtocolName_SeriesDescription". Afterward it will ask user to fill the mandatory fields (in red) for this datatype according to BIDS structure.
- (4) Save the BIDS informations given by the user for this serie in order to process it the same way if new data with same serie is given
- (5) Sort DICOM data in pseudo BIDS architecture under the "BIDS_dir/sourcedata" folder
- (6) Convert sourcedata folder in nifti (.nii.gz) thanks to dcm2niix and sort them in "BIDS_dir/rawdata" folder (will also set up all the required associated files).
Download
Please click on the link below to download the app :
Download BIDS'em ALLYou will also need to install Java 8 runtime (if you don't already have it):
Download Java 8 runtimeFAQ
Yes, the software runs on Windows/Mac and Linux, you just have to launch "bidsemall.jar".
Launch "bidsemall.jar" by double clicking it. In the window just click on the "input dicom directory" button to select the folder containing your dicoms (dicomdir is not required and you can hava as many folder that you want). Then select the output directory (where your BIDS structure will be saved) and click "Convert".
If you already preprocessed the dicom so they are now located in the "BIDS_dir/sourcedata" folder, you can on the main window, only select the output directory and hit convert in order to reperform the conversion/nifti sorting step. Note that you can select in the "Options" panel if you want to reuse previously converted data or reset the conversion.
You can edit the text file "DIC.yml" located in the app directory and modify directly the information here.