[Simnibs-discuss] Simnibs error - could not find tissue probability maps

[Adrianna Giuffre]

Hello

My name is Adrianna Giuffre - I am a PhD candidate at the University of Calgary.
I am using SimNIBS for a current modelling project.
I am having the problems running new head models.

1) I am having troubles running the head models for any of my participants - I keep getting an error message saying : (screen shot attached)

Traceback (most recent call last):

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module>

    main()

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main

    headmodel(sys.argv)

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel

    raise OSError('Could not find tissue probability maps.\n'

OSError: Could not find tissue probability maps.

Probably something went wrong with the Matlab call or SPM

My participant folder has an "org" folder with the T1.nii and T2.nii in them.
I have Matlab installed on my computer. I am not sure if it is an error with where SIMNIBS downloads on my computer - it seems to only download under a "user" - as you can see from the screenshot - it is the only application in the application folder. In my generic application folder - simnibs doesn't show up visually - though when I open it through terminal it does. I am not sure if this is why it cannot find the site-packages within simnibs. I also tried changing the permission of the application (chmod options) and did not have any success.

I also tried installing simnibs on another user on my computer and on another Mac computer and got the same error. I have used simnibs before and have never had this error.

I have tried to fix this over the last few days and watched the tutorial videos - I can't seem to fix the problem. I updated simnibs to the current version. I also uninstalled it and tried installing it again and am having the same issue. This problem has only occurred using this version. I previously ran 25 head models on the previous version and did not have any issues.

Attached are all the screen shots of my error messages and the code I am using to run the headmodels.
mvp1.sh is the script I am using. I tried "headreco all" and headreco all --cat". The headreco_log.html file is also attached.

I appreciate your time and help!
Thank you in advance!

Kind regards,
Adrianna

--

Adrianna Giuffre | PhD Candidate (Neurosciences) | CSEP-CPT
University of Calgary
Calgary Pediatric Stroke Program
Alberta Children’s Hospital
28 Oki Drive NW, Calgary, AB, Canada
T3B6A8
403-955-2471
adrianna.giuffre1 at ucalgary.ca
Program website: www.perinatalstroke.com<http://www.perinatalstroke.com>


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