Installing ISIS-conv on MAC

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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 😉

Installing ISIS-conv on macOS BIG sur (11.5 and later)

Preparation of dependencies

FYou need to have Apple’s Comand line tools installed:

xcode-select --install

You need to set up your mac to be able to copy files to /usr/ sub directories

  • Reboot your mac and during the booting press command+r
  • go to utils -> terminal
  • type csrutil disable
  • type reboot

Installing pre-compile binaries

Download the latest precompiled package from Enrico Reimers isis repository: https://github.com/DerOrfa/isis/releases.

Follow the instructions and execute in the terminal: 

sudo tar -C /usr/local/ --strip-components 1 -zxf isis-core-0.8.0-Darwin-release.tar.gz

Installing ISIS-conv on MAC (10.5 and older)

  • Download the MAC isis package here. (update Aug 2021: Atlassian closed that service, reach out to Renzo Huber renzohuber@gmail.com, for access to the package).
  • Get the file isis-core-0.7.9-darwin.mpkg.zip and 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
  • type csrutil disable
  • type reboot

Since High Siera, the installation will fail as the program is not from and “identified developer” from the Appstore.

Screenshot 2018-11-29 08.00.44.png

It can be installed anyway by opening the System Preferences -> Security & Privacy -> General.

Screenshot 2018-11-29 08.00.54.png

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

On Ubuntu

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

Alternative:

via https://bintray.com/isis-group
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”

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