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NIFD2BIDS

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Alexandre Routier edited this page Mar 15, 2020 · 4 revisions

nifd-2-bids – Conversion of Neuroimaging in Frontotemporal Dementia (NIFD) to BIDS

!!! quote "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.

Dependencies

If you only installed the core of Clinica, this pipeline needs the installation of the dcm2nii and dcm2niix DICOM to NIfTI converters, and of FreeSurfer. You can find how to install these software packages on the installation page.

Downloading NIFD

To download the NIFD dataset you first need to register to the LONI Image & Data Archive (IDA), a secure research data repository, and then request access to the NIFD dataset through the submission of an online application form.

In order to use the converter, you will need to download both the images and the clinical data. To do so, from the main page click on PROJECTS and NIFD. To download the imaging data, click on Download and choose Image collections. In the Advanced search tab, pick the images you wish to download, for example tick MRI to download all the MR images, and then click on SEARCH. In the Advanced search results tab, click Select All and Add To Collection. Finally, in the Data Collection tab, select the collection you just created, tick All and click on Advanced download. We advise you to group files as 10 zip files.

To download the clinical data, click on Download and choose Study Data. Select all the csv files which are present by ticking ALL and click Download. You should get two files: NIFD_Clinical_Data_2017_final_updated.xlsx and DataDictionary_NIFD_2017.10.18.xlsx. One last file is needed, click on Download and choose Image collections. In the Advanced search tab, tick all modalities and all boxes from the Display in result column. Click SEARCH and CSV Download. You should get a file named idaSearch_<date>.csv. Please rename this file to idaSearch_all.csv.

Modalities supported

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

Using the converter

The converter can be run with the following command line:

clinica convert nifd-to-bids dataset_directory clinical_data_directory bids_directory

where:

  • dataset_directory is the path to the original NIFD images' directory;
  • clinical_data_directory is the path to the directory where the following clinical data files are located: NIFD_Clinical_Data_2017_final_updated.xlsx, DataDictionary_NIFD_2017.10.18.xlsx and idaSearch_all.csv;
  • bids_directory is the path to the output directory, where the BIDS-converted version of NIFD will be stored.
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