Preprocessing of fmri data (basic)
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1 Preprocessing of fmri data (basic) Practical session SPM Course 2016, Zurich Andreea Diaconescu, Maya Schneebeli, Jakob Heinzle, Lars Kasper, and Jakob Sieerkus Translational Neuroodeling Unit (TNU) Institute for Bioedical Engineering (IBT) University and ETH Zürich Translational Neuroodeling Unit
2 Goals of this session Go through a preprocessing pipeline in SPM. Learn how to check whether soe basic steps worked. Soe basic file operations in SPM. Save, load and odify batches How to ake your own preprocessing script. Answers to "all" your questions.
3 Preprocessing tools on the SPM GUI and Batch Editor 3
4 The Dataset: Event-related fmri Goal: Investigate Repetition Suppression N tie (scans) N tie (scans) 1 F1 How: Each face presented twice during the session, 26 faous and 26 nonfaous faces 2x2 factorial design Factor Fa(iliarity): long-ter eory, Level: Faous or Unfaous Factor Rep(itition) Level: 1 or 2 Task: Button press to decide fae tie (scans) 1 F tie (scans) Stiulus Onsets all_conditions.at R. Henson et al., Cereb Cortex
5 Slice-Tiing Correction (Teporal Preproc) fmri tie-series Goal: Correct for different acquisition tie of each slice within an iage volue fri.nii How: All voxel tie series are aligned to Slice-Tiing Correction acquisition tie of 1 slice via Sincinterpolation of each voxel s tie series afri.nii Slice-tiing corrected iages 5
6 Spatial Preprocessing fmri tie-series Anatoical MRI TPMs Input Output Segentation Deforation Field y_*.nii Kernel REALIGN COREG SEGMENT NORM WRITE SMOOTH Motion corrected Mean functional (Headers changed) MNI Space GLM 6
7 Realignent fmri tie-series Goal: Correct for subject otion between volues by iniising ean-squared difference How: Rigid-body transforation fri.nii REALIGN Note: Realignent iproves if iages are reoriented in advance (find the origin, change header, use check reg with the canonical iage) fri.nii fri.at rp_fri.txt eanfri.nii (Headers changed) (unchanged) Motion corrected Realignent paraeters Mean functional 7
8 Co-registration Mean functional Anatoical MRI Goal: Match geoetry of functional and structural iages fro sae subject Structural = high-resolution, geoetrically correct iage for later noralisation eanfri.nii Other iages fri.nii COREG struct.nii How: Find affine transforation (rotation/translation/shear/scaling) that axiizes utual inforation (siilarity) between both iages Co-registered fri.nii eanfri.nii Note: The role of functional and structural (Headers changed) iage could be reversed in this operation Reference = header unchanged Source = header will be changed 8
9 Noralisation: Unified Segentation Anatoical MRI Standard Space Tissue Probability Maps Co-registered functional fri.nii struct.nii SEGMENT sp12/tp/tpm.nii NORMALIZE WRITE c1-3struct.nii struct.nii y_struct.nii wfri.nii wstruct.nii Segented Iage Bias-corrected Structural Deforation Fields Noralized Functional (MNI Space) Noralized Structural 9
10 Noralisation I: Copute Segentation/Deforation Fields Anatoical MRI Standard Space Tissue Probability Maps Goal: Match geoetry of subject brain to standard space (for group studies) Integrated with segentation, since apping individual tissue classes is ore robust struct.nii sp12/tp/tpm.nii SEGMENT c1-3struct.nii struct.nii y_struct.nii How: Find non-linear transforation (deforation field) that akes tissue class distribution in structural iage ost plausible Assuing coil inhoogeneity (bias), and deforations of reasonable anatoy Note: uses a Bayesian axiu a posteriori Segented Iage Bias-corrected Structural Deforation Fields estiation, where standard space tissue probability aps (TPMs) are the priors 10
11 Noralisation II: Warp via Write Bias-corrected Structural Deforation Fields Co-registered functional Goal: Write out functional/structural iage in standard space for ultisubject statistical analysis to report findings in coon anatoical struct.nii y_struct.nii fri.nii space (e.g. MNI) NORMALIZE WRITE How: Applies estiated deforation fields fro Unified Segentation to wstruct.nii wfri.nii all functional and structural data Deforation fields have a displaceent vector for each iage voxel that tells where it should be oved to in standard space Noralized Structural Noralized Functional (MNI Space) 11
12 Soothing Noralized Functional (MNI Space) Input Output Goal: Increase sensitivity by reducing wfri.nii SMOOTH swfri.nii Kernel theral noise and inter-subject variability in functional iages Plus a couple of ore sophisticated reasons, e.g. atched-filter theore, soothness of residual rando field for FWE-correction How: Convolution ("Blurring") with a 3D Gaussian kernel Each voxel effectively becoes a weighted average of its surroundings (interpolation) Typical full width at half axiu: 2-3 voxel Soothed Iages (Ready for Stats!) 12
13 SPM Iage File Prefixes xfri.nii/at Prefix Meaning Typicallly applied to a Slice-tiing corrected functional Bias-field corrected (odulated) structural ean Mean of tie-series functional r Re-sliced (change iage atrix, reset hdr) both s Soothed functional u Unwarped (during realign/fieldmap Tool) functional y_ Deforation field structural w Noralized (warped with deforation field) both 13
14 SPM File Operations in Matlab Coand Window Operation Matlab/SPM coand Retrieve ultiple file naes Plot Iage(s) with SPM Load iage header(s) Load Iage Matrix fnaes = sp_select('fplist', pwd, '^sm.*\.ig$'); sp_check_registration(fnaes) hdr = sp_vol(fnaes); X = sp_read_vols(hdr); Inspect Batch in Batch Editor sp_joban('interactive',... atlabbatch); Run Batch fro coand line sp_joban('initcfg'); %1st tie sp_joban('run',atlabbatch); 14
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