#OSIRIX MD STANFORD INSTALL#
#OSIRIX MD STANFORD MANUAL#

In the Info tab, set Executable to Horos (or OsiriX).amework is not included in this repository (the folder is just a placeholder).See Information for developers Things to change after cloning OsiriX: website, github About Brain Imaging Data Structure The plugin development switched from OsiriX to Horos prior to 0.1 release, but it is likely that the plugin will be compatible with both. OsiriX and Horos are DICOM image viewers / database browsers. Not all BIDS suffixes are available in the GUI.įor more details, see the known limitations section of project wiki.Field maps are handled only in the case of one phasediff and two magnitude images (based on the Siemens Trio output).This may include filling in some JSON fields (only the strictly obligatory ones are present) and adding stimulus information.

#OSIRIX MD STANFORD MANUAL#

Please keep in mind that the aim of the plugin is to create the fundamental BIDS structure, and the resulting dataset will most likely require some manual tweaks to become complete.

Usageįor usage instructions, see the project wiki. However, if an executable file named dcm2niix is found in your home directory, Bids Output Extension will use it by default. The dcm2niix executable can be placed anywhere on your computer.

#OSIRIX MD STANFORD INSTALL#

To install dcm2niix, go to dcm2niix releases page and download the executable. Dependencies: dcm2niixīids Output Extension works by launching dcm2niix, which has to be available. Then, proceed with installation as described above. If you trust the plugin, you can remove the 'quarantine' attribute from the Terminal by navigating to the downloaded file and executing xattr -c HorosBidsOutput.horosplugin. On MacOS Catalina and above, the plugin will be blocked by the Gatekeeper ( the developer cannot be verified). Regardless of the installation method, the plugin can then be made available to all users through Horos' Plugins Manager. horosplugin file should launch horos with a prompt and install the plugin for the current user.Īlternatively, the file can be manually placed in: ~/Library/Application Support/Horos/Plugins/. If you have Horos installed, double-clicking the. The plugin allows creation of fundamental BIDS structure from within Horos GUI, based on a mapping between sequence name and BIDS terms entered by user.ĭownload the HorosBidsOutput.horosplugin from the releases page above.

Created during Stanford Center for Reproducible Neuroscience coding sprint 2017.

Osirix md stanford