| Literature DB >> 26578859 |
Rogier A Feis1, Stephen M Smith2, Nicola Filippini3, Gwenaëlle Douaud2, Elise G P Dopper4, Verena Heise3, Aaron J Trachtenberg2, John C van Swieten5, Mark A van Buchem6, Serge A R B Rombouts7, Clare E Mackay3.
Abstract
Resting-state fMRI (R-fMRI) has shown considerable promise in providing potential biomarkers for diagnosis, prognosis and drug response across a range of diseases. Incorporating R-fMRI into multi-center studies is becoming increasingly popular, imposing technical challenges on data acquisition and analysis, as fMRI data is particularly sensitive to structured noise resulting from hardware, software, and environmental differences. Here, we investigated whether a novel clean up tool for structured noise was capable of reducing center-related R-fMRI differences between healthy subjects. We analyzed three Tesla R-fMRI data from 72 subjects, half of whom were scanned with eyes closed in a Philips Achieva system in The Netherlands, and half of whom were scanned with eyes open in a Siemens Trio system in the UK. After pre-statistical processing and individual Independent Component Analysis (ICA), FMRIB's ICA-based X-noiseifier (FIX) was used to remove noise components from the data. GICA and dual regression were run and non-parametric statistics were used to compare spatial maps between groups before and after applying FIX. Large significant differences were found in all resting-state networks between study sites before using FIX, most of which were reduced to non-significant after applying FIX. The between-center difference in the medial/primary visual network, presumably reflecting a between-center difference in protocol, remained statistically significant. FIX helps facilitate multi-center R-fMRI research by diminishing structured noise from R-fMRI data. In doing so, it improves combination of existing data from different centers in new settings and comparison of rare diseases and risk genes for which adequate sample size remains a challenge.Entities:
Keywords: dual regression; independent component analysis; multi-center analysis; resting-state functional MRI; structured noise reduction
Year: 2015 PMID: 26578859 PMCID: PMC4621866 DOI: 10.3389/fnins.2015.00395
Source DB: PubMed Journal: Front Neurosci ISSN: 1662-453X Impact factor: 4.677
Structural and functional scan parameters per scan site.
| TR | 9.8 ms | 2040 ms | 2200 ms | 2000 ms |
| TE | 4.6 ms | 4.7 ms | 30 ms | 28 ms |
| Flip angle | 8° | 8° | 80° | 89° |
| Number of slices/FOV | 140 slices | FOV = 192 cm2 | – | – |
| Number of axial slices | – | – | 38 | 34 |
| Number of volumes | – | – | 200 | 180 |
| Voxel size | 0.88 × 0.88 × 1.20 mm | 1 × 1 × 1 mm | 2.75 × 2.75 × 2.75 mm + 10% interslice gap | 3 × 3 × 3.5 mm |
| Total scan time | 5 min | 6 min | 8 min | 6 min |
FOV, field of view; LUMC, Leiden University Medical Centre; OCMR, Oxford Centre for Clinical Magnetic Resonance Research; TE, echo time; TR, repetition time.
Structural scanning at OCMR was done using a magnetization-prepared rapid gradient echo sequence (MPRAGE).
Participant demographics.
| Age, y | 49.9 (11.5) | 49.8 (11.3) | 0.943 |
| Gender, % Female | 52.8 | 50.0 | 1.000 |
| Education, y | 16.6 (3.2) | 12.6 (2.9) | < 0.001 |
LUMC, Leiden University Medical Centre; OCMR, Oxford Centre for Clinical Magnetic Resonance Research.
Values denote mean (SD);
statistically significant; scores of education level in years were missing for two individuals (both LUMC subjects).
FIX classifications.
| ICs | 36.1 (4.8) | 44.3 (7.9) | < 0.001 |
| Noise ICs | 23.6 (3.9) | 31.8 (8.2) | < 0.001 |
| RSN ICs | 12.6 (3.0) | 12.7 (3.0) | 0.875 |
IC, independent component; LUMC, Leiden University Medical Centre; OCMR, Oxford Centre for Clinical Magnetic Resonance Research.
Values denote mean (SD);
statistically significant.
Figure 1GICA spatial maps before and after FIX. Maps illustrate the 25 GICA networks' most informative orthogonal slices before (A, GICA-1) and after (B, GICA-2) applying FIX. Green frames indicate RSNs; red frames indicate noise networks. Color bar represents Z-scores. GICA, Group-level Independent Component Analysis.
Figure 2GICA spatial maps for statistical analysis. Maps illustrate the 25 GICA networks' most informative orthogonal slices of data before and after applying FIX combined (GICA-3). Green frames indicate RSNs; red frames indicate noise networks. Color bar represents Z-scores. GICA, Group-level Independent Component Analysis.
Figure 3Combined group differences. Maps show statistically significant (p < 0.05) differences between groups: without the use of FIX (A), after the use of FIX (B) and the interaction between FIX and group differences (C) in all (15) RSNs combined. Color bar represents the number of significantly differing networks.