[Simnibs-discuss] hippocampal segmentation to stl

Inês Violante inesviolante at gmail.com
Mon Dec 14 12:51:52 CET 2020

Hi Axel,

Thanks for the quick reply.
I tried that but with no luck. See command line output below.

 nii2msh -ev TIDES_P2T_S1_FreeSf/TIDES_P2T_S1/mri/lHippocampus.nii.gz TIDES_P2T_S1.msh lHipp.msh

[ simnibs ]INFO: Creating tensor visualization

Traceback (most recent call last):

  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 92, in <module>


  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 71, in main

    aniso_tissues=[1, 2])

  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/simulation/cond.py", line 173, in cond2elmdata

    assert len(anisotropy_volume.shape) == 4


Could this be because the volume is smaller than the expected from the T1 mesh?

All the best,


Dr Ines Violante
Lecturer in Psychological Neuroscience
School of Psychology | Faculty of Health and Medical Sciences
Room 32 AC 04
University of Surrey | Guildford GU2 7XH

From: Axel Thielscher <axelt at drcmr.dk>
Date: Friday, 11 December 2020 at 20:39
To: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>, inesviolante at gmail.com <inesviolante at gmail.com>
Subject: Re: [Simnibs-discuss] hippocampal segmentation to stl

Hi Ines,

when you open the nifti-file in freeview, is it then coregistered with the <subid>_T1fs_conform.nii.gz which headreco creates? If not, you can first run freesurfer and use the T1 and T2 which freesurfer stores as input to headreco.

You can then try the nii2msh tool, which puts the data from niftis into the mesh.

Let us know in case you get stuck.

Best regards,


On 12/9/2020 6:40 PM, Inês Violante wrote:

I’ve just tried headreco and it is really cool.
I would like to have a segmentation of the hippocampus in the same space as the meshes generated by headreco.
I have the hippocampus segmentation from freesurfer aligned to the subject space. This is a .nii.gz file

How can I now convert this to stl and have it in  the same space as the other meshes generated by headreco?

Thank you in advance!

All the best,



Simnibs-discuss mailing list

Simnibs-discuss at drcmr.dk<mailto:Simnibs-discuss at drcmr.dk>



Dr. Axel Thielscher

Associate Professor

Danish Research Center for Magnetic Resonance

Copenhagen University Hospital Hvidovre

DK-2650 Hvidovre, Denmark



Department of Health Technology

Technical University of Denmark

DK-2800 Kgs. Lyngby

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