Preprocessing of fmri data

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1 Preprocessing of fmri data Pierre Bellec CRIUGM, DIRO, UdM

2 Flowchart of the NIAK fmri preprocessing pipeline fmri run 1 fmri run N individual datasets CIVET NUC, segmentation, spatial normalization slice timing run 1 slice timing run N coregistration - median fmri Motion estimation resampling run 1 resampling run N scrubbing run 1 scrubbing run N regress confounds run 1 regress confounds run N CORSICA run 1 CORSICA run N default off smoothing run 1 smoothing run N

3 Slice timing correction fmri time TR 7 t t 1 2 series t interleaved mode 1 t 2 temporal interpolation to a single reference time for each volume (cubic spline interpolation) Courtesy of Dr M. Pélégrini-Issac.

4 Motion estimation: within-run volume of reference (median) time time within-run motion parameters : 3 rotations 3 translations for each volume

5 Motion estimation: between-run / within-session RUN 1 between-run motion parameters RUN n between-run motion parameters RUN N time

6 Motion estimation: between sessions SESSION 1 SESSION k SESSION K RUN 1 RUN 1 RUN 1 between-run motion parameters between-session between-run motion parameters between-session between-run motion parameters motion parameters motion parameters RUN n RUN n RUN n between-run motion parameters between-run motion parameters between-run motion parameters RUN N RUN N RUN N time time time Estimation of between-run (between-session) rigid-body motion.

7 T 1 processing: linear coregistration

8 T 1 processing: non-linear coregistration

9 T 1 processing: linear template Linear ICBM template (average of 152 subjects)

10 T 1 processing: linear coregistration Individual structural scan (linear coregistration)

11 T 1 processing: non-linear coregistration Individual structural scan (non-linear coregistration)

12 T 1 processing: nonlinear template Symmetric non-linear ICBM template (average of 152 subjects) release 2009a.

13 T 1 processing: group average Average of 17 subjects (non-linear coregistration)

14 T 1 processing: Flowchart of the CIVET pipeline native MRI stereotaxic MRI brain masking non uniformity corrections brain masking linear registration non uniformity corrections brain masking non linear registration classification Flowchart of the T1 preprocessing.

15 T 1 processing: main outputs raw T1 volume non-uniformity corrected volume linear (lsq9) coregistered volume linear MNI152 template brain mask non-linear coregistered volume non-linear MNI152 template The main outputs of the T 1 processing pipeline.

16 Coregistration between the T 1 and fmri volumes Correct to zero mean, smooth, eresample T1 volume & brain mask iteration 1 : large smoothing smooth : 8,4,8,4,3 step : 4,4,4,2,1 simplex : 8,4,2,2,1 fmri volume & brain mask iteration 1 : large smoothing smooth : 8,4,8,4,3 step : 4,4,4,2,1 simplex : 8,4,2,2,1 Correct to zero mean, smooth iteration 5 : small smoothing iteration 5 : small smoothing 5 iterations progressive fit : LSQ6 coregistration - MINCTRACC (mutual information)

17 Spatial resampling native functional space stereotaxic space - individual volume - non-linear transform - stereotaxic space - average of 40 subjects The transformations to correct for rigid-body motion during the fmri acquisition and the transformation to match the T 1 image and then (non-linearly) coregister into stereotaxic space are all combined, and a single step of spatial resampling is applied.

18 Scrubbing: frame displacement Frame displacement is the sum of absolute displacements in translation and rotation motion parameters. For each frame with excessive FD (here FD> 0.5), four frames are suppressed (the target one + one before + two after, marked with red stars on the figure). The original method was proposed by Power et al. Neuroimage Note that, unlike the original method, only FD is used in NIAK (and not DVARS).

19 Scrubbing: example of impact on the DMN See Power et al. Neuroimage 2012 for more infos.

20 Regress confounds: model

21 CORSICA: sources of structured noise Many sources of space-time correlated noise fluctuations are corrupting fmri time-series: 1/f acquisition noise space-time filtering slice-timing correction motion motion correction Cardiac fluctuations Dagli et al. Neuroimage (1999) Respiratory fluctuations Raj et al. Phys. Med. Biol. (1999) Residual motion McKeown et al. HBM (1998)

22 CORSICA: independent component analysis group 0 group 1 group 2 spatially independent components analysis Perlbarg et al. Magnetic Resonance Imaging, 2007, 25:

23 CORSICA: selection of noise components Flowchart of the CORSICA algorithm for correcting structured noise in fmri Perlbarg et al. Magnetic Resonance Imaging, 2007, 25:

24 CORSICA: effect map x = 0 y = 0 z = Relative variance of estimated structured noise using CORSICA. Average on 40 subjects, 5 tasks per subject. P. Bellec, V. Perlbarg and A. C. Evans, Magnetic Resonance Imaging, 2009, pp

25 Spatial smoothing native resolution smoothed image isotropice Gaussian kernel - 6 mm FWHM

26 Quality control and assessment It is recommended to check the quality of the following steps: Coregistration of the individual T 1 image and the brain template (stereotaxic space). Coregistration of the individual T 1 image and the individual average BOLD volume. Ammount of motion. Complete guidelines: manual/raw/master/qc_manual_v1.0/qc_manual_niak.pdf

27 Quality control and assessment: example

28 Useful links 1 The download page, with this pdf presentation, NIAK releases and the demo dataset 2 The NIAK online user s guide 3 The NIAK project page and developer s guide 4 The PSOM project page

29 License The NIAK project is under an MIT opensource license Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software ), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, IN- CLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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