Translating MATLAB code to Python: Cortical Lesion Finder

[barbrakr]

Cortical Lesion Finder

Barbara A.K. Kreilkamp

Project Description

The high anatomic specificity of MRI may depict focal lesions and can be expertly assessed by visual analysis through neuroradiologists (Von Oertzen et al. 2002). Still, it is important to find ways to improve the diagnostic yield from MRI through optimized MRI protocols, expert neuroradiological assessment and quantitative analysis of post-processed volumetric MRI (Sisodiya et al. 1995, Huppertz et al. 2005).

This project focuses on quantitative analysis to improve detection of focal cortical dysplasia (FCD), which is a common lesion associated with medically refractory epilepsy and often epileptogenic. FCD is a type of cortical malformation that is neuroradiologically characterized by cortical thickening, GM/WM blurring and transmantle signs, which are abnormal extensions of GM towards the ventricles (Barkovich et al. 1997, Huppertz et al. 2005). FCDs are the most common lesions in children and is the third most common lesion after hippocampal sclerosis (HS) and tumors in adult patients.

Within our study, a dedicated epilepsy MRI research protocol including isotropic 3D T1-weighted and FLAIR was performed on patients with medically refractory focal epilepsy, who were deemed to be non-lesional based on previous MRI. The most recent MRIs conducted in context of this study allowed (i) a clinical diagnostic assessment by an experienced neuroradiologist and (ii) the application of an automated quantitative voxel-based lesion detection technique on patients' MRIs in order to find potentially epileptogenic lesions such as FCDs.

I have used MATLAB to program an automatic cortical lesion finder tool and would like to translate it into Python together with you!

Specific goal

• overall: making a python version of the MATLAB-based toolbox
• merge the GUI with the rest of the code
• implement more image processing steps from MATLAB pipeline

Skills required to participate

Creativity for incorporating nipype and nilearn (for voxel-based morphometry)

Coding skills

language	level of expertise required
python	beginner / confirmed / expert
unix command line	beginner / confirmed / expert
MATLAB	beginner / confirmed / expert

software specific sills

software	level of expertise required
SPM	beginner / confirmed / expert
FSL	beginner / confirmed / expert
Freesurfer	beginner / confirmed / expert
Nipype	beginner / confirmed / expert

GIT / GITHUB skills required

level	description
GIT - 1	can commit and push to a repository
GIT - 2	comfortable working with branches and can do a pull request on another repository

Integration

As of now, we only have a limited number of cortical lesions. The idea is to make this project available to clinicians as collaborators, incorporate their feedback and improve the detection rate and usability of the software.

Milestones:

(i) Incorporate the Graphical User Interface into rest of package; (ii) Translate MATLAB/SPM12 algorithms using GitHub packages (iii) Incorporate these steps into the package

Preparation material

• Python programming tutorials
• Proper documenting/commenting
• nipype and nipype introduction
• Not totally necessary but perhaps useful: nilearn, SPM12, CAT12
• Huppertz H.-J., Grimm C., Fauser S., Kassubek J., Mader I., Hochmuth A., et al. (2005). Enhanced visualization of blurred gray-white matter junctions in focal cortical dysplasia by voxel-based 3D MRI analysis. Epilepsy Research, 67(1-2), 35–50. http://doi.org/10.1016/j.eplepsyres.2005.07.009
• Kreilkamp, B.A.K., Das, K., Wieshmann, U.C., Biswas, S., Marson, A.G., Keller, S.S. (2019). Neuroradiological findings in patients with ‘non-lesional’ focal epilepsy revealed by research protocol. Clinical Radiology, 74(1):78.e1–78.e11. http://doi.org/10.1016/j.crad.2018.08.013
• Kreilkamp, B.A.K., Das, K., Wieshmann, U.C., Tyler, K., Kiel, S., Gould, S., Marson, A.G., Keller, S.S. (2017) Voxel-based MRI Analysis Can Assist Clinical Diagnostics in Patients with MRI-negative Epilepsy. Organization of Human Brain Mapping, Vancouver, Canada. http://tiny.cc/VBM_epilepsy

Join Slack channel

@cortical_lesion_finder

GitHub Repository

Cortical Lesion Finder

More References

• Von Oertzen, T.J., Urbach, H., Jungbluth, S., Kurthen, M., Reuber, M., Fernandez, G. et al. (2002). Standard magnetic resonance imaging is inadequate for patients with refractory focal epilepsy. Journal of Neurology, Neurosurgery, and Psychiatry, 73(6), 643-647. http://doi.org/10.1136/jnnp.73.6.643
• Sisodiya, S.M., Free, S.L., Fish, D.R., Shorvon, S.D. (1995) Increasing the yield from volumetric MRI in patients with epilepsy. Magnetic Resonance Imaging 13:1147–1152.
• Barkovich, A.J., Kuzniecky, R.I., Bollen, A.W., Grant, P.E. (1997) Focal transmantle dysplasia: a specific malformation of cortical development. Neurology 49, 1148–1152.

[jonkingseestheworld]

Very useful information and sounds like a very interesting project to me too. Thanks both!

[ofgulban]

Hi @barbrakr ,

Nice project! I thought maybe this example readme.md might be helpful for you to improve yours (installation instructions etc.).

[ofgulban]

Just leaving a reference here for virtual python environments: link.

[barbrakr]

thanks @ofgulban ! :-)

[ofgulban]

Forwarding 2 examples for a simple command line interface:

• This one.
• This one.