nifd-to-bids – Conversion of Neuroimaging in Frontotemporal Dementia (NIFD) to BIDS¶
Description reproduced from the NIFD's LONI Image & Data Archive (IDA) webpage
NIFD is the nickname for the frontotemporal lobar degeneration neuroimaging initiative (FTLDNI, AG032306), which was funded by the NIA and NINDS to characterize longitudinal clinical and imaging changes in FTLD. The imaging and clinical methods are the same for NIFD and for the 4-Repeat Tauopathy Neuroimaging Initiative (4RTNI), which is also available for download from LONI. Controls for NIFD are the same controls as those collected for 4RTNI.
If you only installed the core of Clinica, this pipeline needs the installation of the dcm2niix DICOM to NIfTI converter. You can find how to install these software packages on the installation page.
In order to use the converter, you will need to download both the images and the clinical data for NIFD.
First, you will have to register to the LONI Image & Data Archive (IDA), a secure research data repository, through the submission of an online application form. Once your access is granted, head to the NIFD projects's page and login using your credentials.
Downloading the imaging data¶
To download the imaging data:
Image collectionsin the menubar below.
Advanced Searchtab and configure the appropriate search criteria for your collection. Please, ensure only
NIFDis selected under the
PROJECT/PHASEsection of the form.
MRIshould be selected in the
Modalitysection by default. Select
PETand leave the selector to
ORto download PET imaging data in addition to MRI.
Once all search criteria have been selected, press
SEARCHat the bottom of the form. Your search results should be presented in a new tab named
Advanced Search Results.
Select the desired subjects and scans using the tick boxes displayed in the form or press
Select Allin the top right corner. Press
Add To Collectionto create a new collection from your selection and give it a name. This name will be used as a stem for future downloads.
Data Collectionstab and find your collection within the
My Collectionstree on the left-hand side.
CSVbutton to download the collection metadata in tabular form.
Select the whole collection by ticking
Advanced Download. A download summary should be displayed with the name of the collection, the number of items selected and a dropdown menu to select different groups of file. Depending on the size of the collection, it is advised to download the collection in 5 or 10 files instead of 1 as default.
Upon completion of the download process, create a new folder and move the collection metadata file as well as the content of the archive(s) into it.
Downloading the clinical data¶
To download the clinical data, press
Study Data, tick
NIFD Clinical Data and press download. Once
downloaded, you may move this file to the same location where the imaging data are stored or somewhere else.
Currently, the modalities supported by our converter are:
- T1-weighted MRI
- T2-weighted FLAIR MRI
- Fluorodeoxyglucose (FDG) PET
- Pittsburgh compound B (PiB) PET
- Clinical data and survey (MMSE, CDR, ...)
Using the converter¶
The converter can be run with the following command line:
clinica convert nifd-to-bids [OPTIONS] DATASET_DIRECTORY CLINICAL_DATA_DIRECTORY BIDS_DIRECTORY
DATASET_DIRECTORYis the path to the original NIFD images' directory;
CLINICAL_DATA_DIRECTORYis the path to the directory where the following clinical data files are located:
BIDS_DIRECTORYis the path to the output directory, where the BIDS-converted version of NIFD will be stored.
Citing this converter in your paper¶
Example of paragraph:
Easily access the papers cited on this page on Zotero.