ISIS-conv is a very useful dicom to nii converter from Enrico Reimer. ISIS-conv gets along with a lot of challenging data sets that no other converter (that I know of) can handle so conveniently:
- SMS-data, where individual slices have a non-constant inter-slice distances.
- VASO data with non-constant TRs
- Multi-echo, multi-coil, and Magnitude/Phase data.
There is a Mac-installation package of ISIS-conv. Unfortunately, however, with every IOS update, it has become more complicated to install it.
Since, I spend too much time figuring out how to install it after every update, I am collecting the necessary steps in this Blog post for future reference:
The name of the converter refers to Egyptian god. Don’t type “convert ISIS” into google 😉
- Download the MAC isis package here.
- Get the file
isis-core-0.7.9-darwin.mpkg.zipand unzip it.
Since EL Capitan, during the installation, the libraries can not be placed in the lib folder any more, due to a new flag “restricted”. Hence, the installation might fail. This can be solved with the following steps.
- Reboot your mac and during the booting press command+r
- go to utils -> terminal
- Now, you can try to install the package by double clicking:
Since High Siera, the installation will fail as the program is not from and “identified developer” from the Appstore.
It can be installed anyway by opening the System Preferences -> Security & Privacy -> General.
Clicking on the “Open Anyway” button will allow one to continue with the installation process.
Since 2021, some versions of MACOS require additional settings to be changed.
- Under “System Preferences -> Security & Privacy -> Privacy” grant full access to terminal and the installer.
- execute in terminal
sudo mount -uw /
sudo killall Finder
Then you can run the installer
The usage of isisconv is described here: https://github.com/isis-group/isis/wiki/isisconv
I use it in this script conv.sh
you can build ISIS from scratch:
Here is an description: https://github.com/isis-group/isis/wiki/linux_from_scratch
http://isis-group.github.io/isis/: you might need some packages for that e.g: libghc-bzlib-dev
click to Ubuntu precise -> set me up
after that use apt-get install isis-utils
you might need to include the library path in the bashrc
via ” export LD_LIBRARY_PATH=/usr/local/lib ” “ wart”