Online neuroimaging databases to BIDS converters

Clinica provides tools to curate several publicly available neuroimaging datasets (currently ADNI, AIBL and OASIS) and convert them to BIDS.

Dependencies¶

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

The Alzheimer’s Disease Neuroimaging Initiative¶

Description reproduced from the ADNI's Study Design webpage

ADNI is a global research effort that actively supports the investigation and development of treatments that slow or stop the progression of AD. This multisite, longitudinal study assesses clinical, imaging, genetic and biospecimen biomarkers through the process of normal aging to early mild cognitive impairment (EMCI), to late mild cognitive impairment (LMCI), to dementia or AD. With established, standardized methods for imaging and biomarker collection and analysis, ADNI facilitates a way for scientists to conduct cohesive research and share compatible data with other researchers around the world.

The ADNI study has three phases: ADNI1, ADNI GO and ADNI2. New participants were recruited across North America during each phase of the study and agreed to complete a variety of imaging and clinical assessments. Participants are followed and reassessed over time to track the pathology of the disease as it progresses. Results are then shared by ADNI through USC’s Laboratory of Neuro Imaging’s Image Data Archive (IDA).

The table below summarizes the North American ADNI study target participant numbers, as well as the types of data taken at the different phases. In reality, the total number of study participants vary.

To download the ADNI dataset you first need to register to the LONI Image & Data Archive (IDA), a secure research data repository, and then request access to the ADNI 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.

Note

You do not have to modify the original folder name or rename the clinical data files before using the converter.

Modalities supported¶

Currently, the modalities supported by our converter are:

• T1-weighted MRI
• Diffusion Weighted Imaging (DWI)
• Fluorodeoxyglucose (FDG) PET
• Florbetapir (AV45) PET

Using the converter¶

Warning

The command line is being finalized.

The converter can be run with the following command line:

clinica convert adni-to-bids dataset_directory clinical_data_directory bids_directory


where:

• dataset_directory is the path to the original ADNI images's directory.
• clinical_data_directory is the path to the directory where the csv file with the clinical data is located.
• bids_directory is the path to the output directory, where the BIDS-converted version of ADNI will be stored.

Optional parameters¶

The converter offers the possibility of converting only the clinical data (once that the images are in the BIDS format) using the optional parameter -c.

Due to the high computational time requested for converting all the modalities of the whole ADNI dataset, it is possible to convert a single modality at the time using the parameter -m with one of the following values:

• T1 for the T1-weighted MRI
• DWI for Diffusion Weighted Images (DWI)
• PET_FDG for the Fluorodeoxyglucose (FDG) PET
• PET_AV45 for the Florbetapir (AV45) PET

Is also possible to provide the path a .txt file with the list of subjects to convert using the optional parameter -s.

clinica convert adni-to-bids -h

Known errors
• T1

Subject sub-ADNI031S0830 for session ses-M48 folder contains sub-ADNI031S0830_ses-M48_T1w_Eq_1.nii

Subject sub-ADNI029S0845 for session ses-M24 folder is empty
Subject sub-ADNI094S1267 for session ses-M24 folder is empty
Subject sub-ADNI029S0843 for session ses-M24 folder is empty
Subject sub-ADNI027S0307 for session ses-M48 folder is empty
Subject sub-ADNI057S1269 for session ses-M24 folder is empty
Subject sub-ADNI036S4899 for session ses-M03 folder is empty


• DWI

Subject sub-ADNI016S4638 for session ses-M00 folder contains sub-ADNI016S4638_ses-M00_dwi_Eq_1.nii

Subject sub-ADNI029S4585 for session ses-M48 has wrong b-val/b-vec file
Subject sub-ADNI029S2395 for session ses-M60 has wrong b-val/b-vec file
Subject sub-ADNI029S0824 for session ses-M108 has wrong b-val/b-vec file
Subject sub-ADNI029S0914 for session ses-M108 has wrong b-val/b-vec file
Subject sub-ADNI029S4384 for session ses-M48 has wrong b-val/b-vec file
Subject sub-ADNI029S4385 for session ses-M48 has wrong b-val/b-vec file
Subject sub-ADNI094S4630 for session ses-M06 has wrong b-val/b-vec file
Subject sub-ADNI094S4649 for session ses-M06 has wrong b-val/b-vec file
Subject sub-ADNI029S5219 for session ses-M24 has wrong b-val/b-vec file

Subject sub-ADNI027S2219 for session ses-M36 has wrong dimensions (256 x 256 x 2013)
Subject sub-ADNI129S2332 for session ses-M12 has wrong dimensions (256 x 256 x 1549)


• FDG PET

Subject sub-ADNI941S1195 for session ses-M48 folder is empty
Subject sub-ADNI005S0223 for session ses-M12 folder is empty
Subject sub-ADNI037S1421 for session ses-M36 folder contains NONAME.nii
Subject sub-ADNI037S1078 for session ses-M36 folder contains NONAME.nii


• AV45 PET

Subject sub-ADNI128S2220 for session ses-M48 folder contains sub-ADNI128S2220_ses-M48_task-rest_acq-AV45_pet_Eq_1.nii


AIBL to BIDS¶

The Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing¶

Description reproduced from the AIBL's Study Design webpage

The Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL) seeks to discover which biomarkers, cognitive characteristics, and health and lifestyle factors determine the development of AD. Although AIBL and ADNI have many of the same goals, there are differences between the two projects. Read more about the AIBL study from their website.

Study Participants AIBL has enrolled 1100 participants and collected over 4.5 years worth of longitudinal data:

• 133 MCI patients
• 768 comparable healthy controls

Data AIBL follows ADNI 1 protocols. Available data includes:

• Clinical and cognitive data
• Image data: MRI, PET
• Biomarkers data: blood, genotype, ApoE
• Dietary/lifestyle assessment

To download the AIBL dataset you first need to register to the LONI Image & Data Archive (IDA), a secure research data repository, and then request access to the AIBL dataset through the submission of an online application form. If you already have an access for ADNI, you can download AIBL with the same account.

In order to use the converter, you will need to download both the images and the clinical data.

Note

You do not have to modify the original folder name or rename the clinical data files before using the converter.

Modalities supported¶

Currently, the modalities supported by our converter are:

• T1-weighted MRI
• Pittsburgh compound B (PiB) PET
• Florbetapir (AV45) PET
• Flutemetamol (FLUTE) PET

Using the converter¶

The converter can be run with the following command line:

clinica convert aibl-to-bids dataset_directory clinical_data_directory bids_directory


where:

• dataset_directory is the path to the original AIBL images's directory.
• clinical_data_directory is the path to the directory where the csv file with the clinical data is located.
• bids_directory is the path to the output directory, where the BIDS-converted version of AIBL will be stored.

OASIS to BIDS¶

The Open Access Series of Imaging Studies¶

Description reproduced from the OASIS' webpage

The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN).

The "Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults" set consists of a cross-sectional collection of 416 subjects aged 18 to 96. For each subject, 3 or 4 individual T1-weighted MRI scans obtained in single scan sessions are included. The subjects are all right-handed and include both men and women. 100 of the included subjects over the age of 60 have been clinically diagnosed with very mild to moderate Alzheimer’s disease (AD). Additionally, a reliability data set is included containing 20 nondemented subjects imaged on a subsequent visit within 90 days of their initial session.

You can download the OASIS dataset here. You will need to download the dataset named OASIS: Cross-sectional MRI Data in Young, Middle Aged, Nondemented and Demented Older Adults and the .xls file with the clinical data.

Note

You do not have to modify the original folder name or rename the clinical data file before using the converter.

Modalities supported¶

Currently, the converter converts only the T1-weighted MRI images.

Note

The T1-weighted MRI selected for the conversion is the one located in the subfolder PROCESSED/MPRAGE/SUBJ_111.

Using the converter¶

The converter can be run with the following command line:

clinica convert oasis-to-bids  dataset_directory clinical_data_directory bids_directory


where:

• dataset_directory is the path to the original OASIS images's directory.
• clinical_data_directory is the path to the directory where the xls file with the clinical data is located.
• bids_directory is the path to the output directory, where the BIDS-converted version of OASIS will be stored.

Note

In order to improve the readability, the BIDS subject id is different from the original OASIS id of the subject. Indeed, the BIDS subject id is so defined:

sub-OASIS1+ original numerical id of the subject

Example: If the original subject id is OAS1_0001_MR1, since the numerical id is 0001, the final BIDS id will be sub-OASIS10001.