I’m embarking on a new role as an image processing specialist within a research group that’s keen on utilizing SPM12 for a sizable dataset of PET images, totaling around 150 scans. My background is in biomedical engineering, and I’ve been exploring various approaches to implement SPM12 analysis effectively. I’m eager to engage in discussions regarding the merits and drawbacks of different platforms and software options available. This is in addition to the tutorials provided within MATLAB itself, which I’m still in the process of examining. I’d greatly appreciate your insights and recommendations on where to begin.
The platforms I’ve identified that support SPM12, based on their documentation, are as follows:
- Neurodesk - with Nipype.
- Clinica - BIDS app (i think).
- Matlab (the source of SPM12) and standalone SPM12.
Furthermore, I’ve come across other platforms that appear intriguing for both project sharing and potential development, such as:
In my exploration of Neurodesk, I’ve discovered that it allows me to employ SPM12 pipelines within a Colab Jupyter notebook. This is particularly interesting as it enables cloud-based work, offering advantages like reproducibility and shareability. It also allows me to leverage machine learning (via SKlearn) and artificial intelligence (using TensorFlow) algorithms and pipelines for making inferences. This aligns well with one of our research objectives.
Regarding the Clinica platform, I’ve found it to offer a straightforward implementation of SPM12, requiring minimal calibration knowledge. They primarily utilize the GLM and provide user-friendly visualization of results through their pipelines. Additionally, there’s ClinicaDL, a deep learning extension, for those interested in exploring this avenue.
I admit that I haven’t fully grasped the capabilities of Brainlife and NeuroHub. While both claim to support Jupyter notebooks and development features, I couldn’t readily locate them in my initial exploration. Also, there is no documentation that i could make SPM12 work on these platforms.
In conclusion, I believe that Neurodesk with Nipype could be a more straightforward and efficient solution for implementing SPM12 on this dataset. This is especially appealing since I can design workflows and then apply them to all PET images, avoiding manual processing, which appears to be the case with Clinica.
Your insights and recommendations on these platforms and any additional tips or experiences you can share would be immensely valuable to me as I embark on this exciting endeavor. Thank you!