COBMAN: Comprehensive Open Brain Map Archive Network

COBMAN  is a network of FTP and web servers around the world that store identical, up-to-date, versions of anatomical experiments and data submitted to be displayed on openbrainmap.org. COBMAN preferentially accepts experiments that have already been subjected to peer-review and only in rare occasions data will be considered before peer-review. In cases a user needs[...]

Directories, files and paths

Learning objectives: How to do basic navigation in directories and files using R console Writing a for-loop to iterate over directories Vectorizing the for-loop using lapply() Applying any function automatically to a set of images inside folders using the above CONTENT: Background Iteration through for loops Vectorization in R Functions Conclusions Background When you open[...]

Installing wholebrain on Ubuntu/Debian

Install R, FFTW and OpenCV 3 Install STAN from within R Install wholebrain from within R Install R, FFTW and OpenCV 3 Install from terminal using apt: sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev sudo apt-get -y install r-base sudo apt-get install fftw3 fftw3-dev pkg-config WholeBrain requires OpenCV 3.0.0 or higher, currently sudo apt-get for[...]

LC_CTYPE_error

When you open up R do you see errors like the following appear in red: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_COLLATE failed, using "C" 3: Setting LC_TIME failed, using "C" 4: Setting LC_MESSAGES failed, using "C" 5: Setting LC_PAPER failed, using "C" To fix this on Mac OSX do the following: Close[...]

Installing wholebrain on macOS

Since WholeBrain heavily relies on STAN for statistical computations the following instructions are somewhat adapted from the installation of rstan. Install or Upgrade R 1.1 Check if you have R installed on your Mac. 1.2: Check if you need to upgrade 1.3: Install or upgrade R Install Xcode and its C++ Toolchain 2.1 Determine which version of OS[...]