Identification of the hemodynamic response in fMRI

May 26, 2009 - hemodynamic response in fMRI. Part III: The pyHRF ... May 26th, Marseille. fMRI analysis with PyHRF ... BOLD data. - seconds. - separator : ...
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Identification of the hemodynamic response in fMRI Part III: The pyHRF software P. Ciuciu1,2 [email protected]

1: CEA/NeuroSpin/LNAO

May 26, 2009

www.lnao.fr

2: IFR49

JIRFNI- “advanced course”, Marseille May 26th, Marseille

PyHRF package

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Outline

General framework Implementation and requirements Setup and use cases Viewer overview

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fMRI analysis with PyHRF

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t t t

PyHRF ●

Parcellation

= n-ary mask (0 label = background) ● ●

from SPM beta maps from 4D fMRI series

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fMRI analysis with PyHRF

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t t t

HRF

PyHRF ●

Parcellation

= n-ary mask ●(0 label = background) ●

● ● ●

from SPM beta maps from 4D fMRI series

contrasts

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Package description Mainly command line Setup with XML files Interactive dedicated viewer Python and C Time issues: parcellation : several minutes JDE : 1 to 2 hours (can be parallelized)

Available at: $P4/neurospy-.../ ⇒ $python setup.py install May 26th, Marseille

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Dependencies gsl

scipy

numpy

fff PyHRF clustering

viewer

PyQt

JDE

PyXML

pynifti

SIP Qt

nifticlib May 26th, Marseille

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Dependencies gsl

scipy

numpy

fff PyHRF clustering

viewer

PyQt

JDE

PyXML

pynifti

SIP Qt

nifticlib May 26th, Marseille

Dependencies (versions)

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fff (snapshot SVN may 2008) GSL 1.9 numpy 1.0 scipy 0.5.2 PyXML 0.8.4 nifticlib 1.0 pynifti 0.20070930.1 PyQt 3.17.3 Qt 3.3.6 SIP 4.7 May 26th, Marseille

Use cases

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Parcellation JDE Viewer

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Parcellation

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$pyhrf_clus_buildcfg

clustering.xml

$pyhrf_clus_run parcellation.nii May 26th, Marseille

Use cases

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Parcellation JDE Viewer

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Joint Detection-Estimation

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$pyhrf_jde_buildcfg

detectestim.xml

$pyhrf_jde_estim -v1 session0_pm_hrf.nii session0_pmNRL_condition_audio.nii session0_pmNRL_condition_audio.nii ...

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Joint Detection-Estimation

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$pyhrf_jde_buildcfg

detectestim.xml

Data definition

Model parameters $pyhrf_jde_estim -v1 session0_pm_hrf.nii session0_pmNRL_condition_audio.nii session0_pmNRL_condition_audio.nii ...

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Joint Detection-Estimation

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detectestim.xml – Data definition

- seconds - separator : space parcellation with positions excluded during analysis (output file)

Input parcellation BOLD data - seconds - separator : space - if empty : spike stimuli

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Joint Detection-Estimation

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detectestim.xml – Model definition (1)

Drift base type ('polynomial' or 'cosine') Drift parameter: polynom order or cut-off frequency

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Joint Detection-Estimation

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detectestim.xml – Définition du modèle (2)

Amount of spatial correlation (between 0.3 et 0.7) Contrast definition Separator: “;” If no contrast: “;” Boolean flags for outputs

Constraint of HRF=0 at first and last time position (boolean) Boolean flag for the HRF estimation. If 0 : use of a fixed canonical HRF May 26th, Marseille

Joint Detection-Estimation ●

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Multi-session aspect

$pyhrf_jde_buildcfg -s homoscedastic

$pyhrf_jde_buildcfg -s independent

Two different xml setup files May 26th, Marseille

Joint Detection-Estimation

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$pyhrf_jde_buildcfg

detectestim.xml

$pyhrf_jde_estim -v1 session0_pm_hrf.nii session0_pmNRL_condition_audio.nii session0_pmNRL_condition_audio.nii ... May 26th, Marseille

Use cases

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Parcellation JDE Viewer

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Viewer

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$pyhrf_view session0*

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Viewer $pyhrf_view session0*

Data browser (slice definition)

current slice view

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Viewer Data browser (slice definition)

current slice view

Slice dimension

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Viewer Data browser (slice definition)

current slice view

Crop to mask

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Viewer Data browser (slice definition)

current slice view

Slice axes selection

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Viewer Data browser (slice definition)

current slice view

Mode 2D: image (matrix)

Mode 1D: curves May 26th, Marseille

PyHRF package – in factory

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Methodological developments ➢

Unsupervised spatial regularization



Habituation modeling



Model comparison

Software developments ➢

Integration to the fMRI Brainvisa toolbox



User friendly parallel system



Scriptable API



Port of the matlab HRF toolbox: L. Risser's work. May 26th, Marseille

Acknowlegdments

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This work was partly supported by grants from Région Ilede-France Special thanks to: Thomas Vincent Anne-Laure Fouque Laurent Risser Stéphane Sockeel

Sophie Donnet

May 26th, Marseille