[Simnibs-discuss] hippocampal segmentation to stl

[Axel Thielscher]

Dear Ines,

the description in the simnibs documentation is not very clear, I am 
sorry for this. You can use nii2mesh -h to get a bit more information 
(not not much though). Please try calling it without the -ev.

Best regards,

Axel

On 12/14/2020 12:51 PM, Inês Violante wrote:
>
> 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>
>
> main()
>
> 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
>
> AssertionError
>
> Could this be because the volume is smaller than the expected from the 
> T1 mesh?
>
> All the best,
>
> Ines
>
> --
>
> 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,
>
> Axel
>
> On 12/9/2020 6:40 PM, Inês Violante wrote:
>
>     Hello,
>
>     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,
>
>     ines
>
>
>
>     _______________________________________________
>
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>
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>
>     https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss  <https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss>
>
> -- 
> Dr. Axel Thielscher
> Associate Professor
> Danish Research Center for Magnetic Resonance
> Copenhagen University Hospital Hvidovre
> DK-2650 Hvidovre, Denmark
> www.drcmr.dk  <http://www.drcmr.dk>
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngby
> http://www.healthtech.dtu.dk/  <http://www.healthtech.dtu.dk/>
>
> -->
>
-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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