image reconstruction server

[Skander Salah]

Hi everyone,

I am facing issues with the image reconstruction server: as shown in the screenshot below, in JEMRIS Simulation GUI, choosing "image" from the dropdown list keeps showing "no bart reco found".

 

Pressing "start reco" results in the following warning message in Matlab terminal: 

I installed JEMRIS using source code (downloaded from git) and I did install Docker and Conda before installing JEMRIS as stated in the Installation documentation.

Cmake successfully creates the conda environment (which I activate before make and make install) and pulls the docker image. 

From what I understood from the Download documentation, "installing JEMRIS from source code will automatically install the server" so what am I missing or what am I doing wrong? 

Cheers

Skander

[tony.s...@gmail.com]

Dear Skander,

Which OS are you using? (Mac or Linux). The problem is to find the conda environment from Matlab. We did not find a better way then running the bashrc script (or profile), assuming that it launches the environment (see lines 432-435 in JEMRIS_sim.m). Obviously, this fails if you are not using bash; then you have to find a different way for your system.  Please let me know if you found a solution. We are still searching for a more general solution ... our approach works on Mac and Linux with bash as default shell.

Best,

Tony

[Skander Salah]

Dear Tony,

thank you very much for your reponse, it did help me find a solution for the issue. I will describe the fixes here in detail so it maybe helps fellow users who might face the same thing.

First to answer your question, I am using Linux (Ubuntu 18.04).

First I needed to change ".bash_profile" into ".profile" in JEMRIS_sim.m, line 432 . I am not knowledgeable of the reasons, but I found the second but not the first in my /home/user/ path.

And then I faced the following conda issue https://github.com/conda/conda/issues/7980. And I found the solution for me was to add "source ~/anaconda3/etc/profile.d/conda.sh" in front of "conda activate ismrmrd_client" in line 433.

After these changes, the error message "conda environment with client not installed" disappeared. But I got the following error message: "bart reco not successful - check gui dump for error message". The error in the GUI was "activate does not accept more than one argument ['ismrmrd_client`, `client.py`, `-c`, `bart_jemris`, `-o`, `gui_reco.h5`, `-G`, `images`, `signals_ismrmrd.h5` ] " which was fast to solve by adding a missing "&&" in line 448 between ',conda_cmd,' and ',client_cmd,' .

Now the image reconstruction server works fine.

Thank you very much for your answer and foremost for all your work and efforts into this very valuable tool.

Cheers

Skander