Open barbrakr opened 4 years ago
Very useful information and sounds like a very interesting project to me too. Thanks both!
Hi @barbrakr ,
Nice project! I thought maybe this example readme.md might be helpful for you to improve yours (installation instructions etc.).
thanks @ofgulban ! :-)
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
Skills required to participate
Creativity for incorporating nipype and nilearn (for voxel-based morphometry)
Coding skills
software specific sills
GIT / GITHUB skills required
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
Join Slack channel
@cortical_lesion_finder
GitHub Repository
Cortical Lesion Finder
More References