Overview of fmri Analysis Software. McConnell BIC Open Methods Meetup January 13th 2013

Transcription

1 Overview of fmri Analysis Software McConnell BIC Open Methods Meetup January 13th 2013

2 FSL Michael Ferreira

3 Outline Introduction MRI scanners and fmri equipment FSL Image formats and conversion FSLView and FEAT FSL at the BIC Support Links

4 Introduction Research Assistant maintain fmri stimulation and subject monitoring equipment for the MRI scanners assist fmri researchers with the development and implementation of new protocols introduce researchers to fmri statistical analysis software packages and provide ongoing support maintain laboratory facilities for, and assist in the preparation of, MRI phantoms

5 Hardware 1.5T Siemens Sonata and 3T Siemens Tim Trio Scanner Imaging Coils: 32 Ch, 12 Ch, 8Ch, Neck Coil, Spine Coil, Extremity Coil (Knee Coil), Wrist Coil, Large and Small Flex Surface coils

6 SENS S14 Audio System

7 SR Research Eyelink

8 Current Designs Fiber Optic Response Pad

9 Hardware... SENS SR14 ear insert audio system SR research Eyelink 1000 Eye tracker Current Designs Response Pads 2 XGA (1024x768) LCD projectors Siemens Physiological Monitoring Unit ECG Pulse Respiration log files with scan markers

10 FSL Imaging data provided in DICOM and MINC formats FSL uses the NIFTI (.nii) format conversion to NIFTI from DICOM MRIcro conversion to NIFTI from MINC mnc2nii

11 OMM Tip: mnc2nii mincreshape +direction \ -dimsize xspace=-1 \ -dimsize yspace=-1 \ -dimsize zspace=-1 \ -dimorder time,zspace,yspace,xspace \ -float infile.mnc outfile.mnc

12 FSL

13 FSL by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) at Oxford University FSL or FMRIB Software Library analysis of MRI, fmri and DTI scans available for Linux, Mac, and VMware virtual machines for Windows installed at the BIC type fsl to launch the GUI

14 FSL: Tools Functional MRI FEAT, MELODIC, FABBER, BASIL Structural MRI BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, fsl_anat Diffusion MRI FDT, TBSS, EDDY, TOPUP Other FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, PNM

15 FSLView MNI 152 Model

16 FSLView 3D Rendering

17 FSLVIEW

18 FSLView view 3D/4D Nifti images fmri, dti, anatomical, atlases, 3D rendering check your raw data movie mode to cycle through a timeseries motion, ghosting, artefacts overlays (anatomicals, stats, atlases) multiple overlays, used like layers in GIMP/PS must have the same dimensions as the main image variety of colour maps available lacks spectral mode like Display/register

19 FEAT ( Feat, Feat_gui )

20 FEAT: Pre-stats

21 FEAT: Stats

22 FEAT: Model Setup

23 FEAT: Post-stats

24 FEAT: Registration

25 FEAT: Report

26 FEAT: Report

27 FEAT at the BIC: SGE batch execution is scheduled on a system of networked computers faster than running only on your local machine for local execution, disable batch: tcsh: unsetenv SGE_ROOT bash: unset SGE_ROOT try using bash instead of a tcsh shell tcsh users may need a custom fsl.csh settings file

28 BIC and FSL Support BIC FSL

29 Thanks!

30 AFNI Benjamin Elgie

31 AFNI Intro AFNI is an fmri software suite developed by a group at the NIH It runs on Linux systems using libxp, tcsh, PyQt4 and R It runs on Mac OSX using Xcode, fink, tcsh, PyQt, and R

32 AFNI components AFNI consists of 3 principal components: A GUI used primarily for viewing data A collection of command-line scripts A parallel surface analysis package (SUMA)

33 AFNI GUI The AFNI GUI is a major part of the software Can be used for viewing data Can also conduct certain on the fly analyses

34 AFNI GUI 2

35 AFNI GUI 3

36 AFNI Scripts This is a set of scripts which can either be run from the command line or from a script using tcsh They typically take as input.1d files, or.head &.brik pairs. AFNI is increasingly able to process NIFTI format files as well.

37 AFNI Scripts 2 AFNI also provides several ways of processing data besides a custom-written script afni_proc.py asks a series of questions and generates a processing scripts based on your responses uber_subject.py is the GUI version of this script, and can also be used to run the script

38 AFNI processing Convert to AFNI format using 3dMINCtoAFNI (making sure to check that the TR is maintained, might need to correct with 3drefit) Can also create files from DICOMs using to3d, but sometimes easier to use a utility program to create an image file

39 AFNI processing 2 1. Strip skull from anat file and align to an epi volume 2. Volume registration (includes recording of motion parameters and selection of TRs for censoring) 3. Despiking 4. Smoothing 5. Create masks 6. Re-scaling BOLD signal 7. Alignment to standard space

40 AFNI Ordinary/Generalized LS Can use either 3dDeconvolve or 3dREMLfit 3dDeconvolve takes as input 3d+time files and stimulus timing files (.1D format) and outputs least-squares estimates of betas, t-stats for betas, partial and full F-stats, and optionally IRFs, and the fitted and residual time series 3dREMLfit takes the model created by 3dDeconvolve and runs while correcting for serial autocorrelation in the noise

41 AFNI Ordinary/Generalized LS 2 There are a lot of different response models that can be used (BLOCK, TENT, GAM etc) Stimuli can be duration- and amplitude- modulated Important - AFNI uses an implicit baseline, so any portion of the time-series not covered by a response model is assumed to be part of the baseline

42 AFNI Group Analysis AFNI has many ways to approach group-level analyses T-tests, ANOVA/ANCOVA, mixed-effects metaanalysis (MEMA), linear mixed-effects (LME), multivariate modelling (MVM)

43 Other capabilities Resting-state and connectivity analysis - seed-based (simple, context-dependent, and Granger causality) - ROI-based (Granger causality and structural vector autoregression) DTI analysis Some MVPA support

44 Major advantages of AFNI - Extremely flexible and customizable - Very responsive team - Many ways to approach the same data

45 Disadvantages of AFNI - Steep learning curve - Easy to use the wrong function or approach - Requires a good understanding of each step in a processing pathway

46 SPM Laureline Arnaud

47 fmri analysis with SPM Free, widely used, a lot of documentation, wikibook, tutorials, datasets etc.

48 fmri analysis with SPM SPM = Matlab scripts Windows, MAC, Linux User interface GUI : click, no need to know any programming or Command-line: matlab programming Batch

49 The main steps of fmri analysis Preprocessing 1st level : Individual level analysis 2nd level :Group analysis

50 The main steps of fmri analysis Preprocessing realign slice timing coregister segment normalize smooth

51 SPM Graphical User Interface Set the parameters in a few clicks Help section at the bottom of the window

52 The main steps of fmri analysis 1st level : Individual level analysis Model specification and estimation 2nd level :Group analysis Factorial Design : one or two sample T-tests, paired T-test, Multiple regression, one way ANOVA, Full factorial, Flexible factorial. Definition of covariates, masking etc.

53 Save some clicks : batch (without matlab programming) Utilities : Batch

54 Save some clicks : batch (without matlab programming) Documentation Reproducibility Unattended execution Multiple batches

55 Utilities : 2 more examples Display Check Reg

56 Utilities : Display facility

57 Utilities : Check Reg facility

58 Command lines / Matlab scripts

59 Screen captures

60 Screen captures

61 Toolboxes Task or rest based functional connectivity VBM Viewing tools (xjview, BrainNetView er) SPM anatomy toolbox (probabilistic cytoarchitecto nic maps) etc.

62 How to get started? SPM website Download SPM 8 (Software) html Manual (Documentation)

63 How to get started? SPM website Dataset (Data) - PET - epoch fmri - event-related fmri - multi-subject analysis - fmri : Bayesian comparison of DCMs - EEG Single Subject Mismatch Negativity - Multimodal faces (MEG,EEG,fMRI) - Fieldmap tollbox

64 Thanks! Interested in creating a SPM user group? laureline.arnaud@mail.mcgill.ca

65 Ideas for our next Open Methods Meetup?