### Kia ora! This is SamSrf X SamSrf stands for **"Seriously Annoying Matlab Surfer"** It is up to you to decide which aspect of it you find seriously annoying... ----- #### Standalone app We are now up to version 10, which is why the toolbox is now called SamSrf X. This includes a new GUI that should make many basic analyses much more user-friendly & convenient. **SamSrfX GUI is available as a standalone app that you run without any Matlab knowledge** (but you need to install the free Matlab Runtime Environment to run it). ----- #### Important Notes While we conducted extensive tests (mostly on Matlab R2020a&b, the latest version was tested on R2023b), but you always encourage you check your data. In general, we recommend using the latest version because it contains the latest features and bug fixes. SamSrf 9 was an overhaul of the forward-modelling pipeline, which *dramatically* improves the speed but also changes the results somewhat. *Results are therefore not directly comparable to versions prior to SamSrf 9!* **As of version 9.6, SamSrf defaults to using 32-bit (single) data type for maps** This improves the speed of pRF model fitting and also halves the amount of disc space required. However, the results are not identical. The discrepancies mostly affect poor model fits but you may want to check your data to see if this update works for you. You can force SamSrf to use 64-bit (double) data by setting *"def_64bit": true* in *SamSrf_defaults.json*. ------ #### What is SamSrf and what do I need? SamSrf allows you to conduct a range of pRF analyses, including model-free pRF and connective field analyses, and also supports a number of other surface-based analyses of neuroimaging data. We aimed to make a user-friendly set of tools for plotting surface maps and for manual delineation of brain regions. Unless you are using the standalone app, SamSrf requires MATLAB and for the full functionality you also require FreeSurfer. We typically use the 3D reconstructions of the cortical surface created in FreeSurfer and you can also use FreeSurfer for your entire preprocessing pipeline. Due to our Queen Square origins, we typically use it in combination with SPM and some functions call SPM routines (SPM12 is advised). It should however be flexible and can be used with FSL or AFNI or other packages provided you can produce functional data in 4D NII format. In fact, as of version R2017b, Matlab supports reading NII files directly. You can use this functionality by downloading the NatMatlabNi4SamSrf mini-toolbox which simply overrides SPM's functions for reading/writing NII files. This is not the most elegant solution but it allows you to use NII in SamSrf completely without SPM but without requiring us to support multiple different I/O methods. Please note that GII surface data file support currently requires SPM though. (Support for NII & GII files is however intergrated in the standalone GUI app). It should also be possible to use surface meshes not created in FreeSurfer or use volumetric data, although functionality will then be limited. ----- #### Contact Us Please contact Sam (or someone from the lab) if you have any questions or spot any problems. However, please be advised that in the interest of our time, sanity, and healthy family-lives, we do not usually provide extensive tech support to people unless we collaborate with them directly. We are developing this toolbox in our free time and mainly for the purposes of our own research. You are free to use this code but **we will not take feature requests and we will deal with problems only when/if it is a priority for us**. Feel free to create your own branch on GitHub & modify the toolbox for your own needs. ------