[FieldTrip] ft_prepare_mesh ERROR

[Arjen Stolk]

Just in case anyone experiences the same or a related issue in the future,
Toshiki and I solved the problem for him, adjusting ft_prepare_mesh_cortexhull
in the main repository
<https://github.com/fieldtrip/fieldtrip/pull/819>. Simply
re-download/pull if you had the same issue.
Arjen

On Fri, Sep 28, 2018 at 10:50 PM Arjen Stolk <a.stolk8 at gmail.com> wrote:

> Dear Toshiki,
>
> From that error, it seems your version of Freesurfer is referencing
> libraries that do not exist while executing the *mris_fill *command. To
> rule out that the issue is due to the call to *mris_fill* being made from
> within the matlab environment as *prepare_mesh_cortexhull* does, you
> could try to call *mris_fill* directly from within a terminal and see if
> it replicates, as follows:
>
> export FREESURFER_HOME=/Applications/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> mris_fill -c -r 1 path_to_freesurfer/surf/lh.pial tmp.filled.mgz
>
>
> If that reproduces the error, it might be worth consulting the
> Freesurfer development team concerning this. A similar issue was reported
> here
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050544.html>,
> but it doesn't look like a fix has been suggested. Alternatively, you
> could try a different version of Freesurfer for creating the cortical hull
>  (freesurfer-Darwin-lion-stable-pub-v5.3.0 runs fine on my mac). Hope
> this helps,
> Arjen
>
>
> On Sep 25, 2018, at 12:13 AM, 岡留敏樹 <tokadome at neuro.med.kyushu-u.ac.jp>
> wrote:
>
> Hello fieldtrip experts,
>
> when trying to run ‘ft_prepare_mesh’ command from fieldtrip with MATLAB R2018a, I run into the error below.
>
> I was preprocessing MRI date according with the paper ’Nature Protocol 2018; 13: 1699-1723. http://doi.org/10.1038/s41596-018-0009-6 ‘.
>
> I’m running this on a iMac, macOS High Sierra 10.13.6, with fieldtrip-20180909, freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c.
>
> From past archives, I think this is because of SIP. So I disabled SIP of OSX, but I run into same errors.
> I tried different subjects, which caused similar errors.
>
> Any ideas would be greatly appreciated, thank you!
>
>
> [CODE]
>
> cfg = [];
>
> cfg.method = ‘cortexhull’;
>
> cfg.headshape = <path to freesurfer/surf/lh.pial>;
>
> cfg.fshome = <path to freesurfer home directory>;
>
> hull_lh = ft_prepare_mesh (cfg);
>
>
> [ERROR]
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>
>   Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> mris_fill -c -r 1 /Users/okadometoshiki/Desktop/SubjectUCI29/freesurfer/surf/lh.pial /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz: Aborted
> reading filled volume...
> gunzip: can't stat: /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz (/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz.gz): No such file or directory
> ERROR: problem reading fname
>
>
>
> ========
>
> Toshiki Okadome
>
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> https://doi.org/10.1371/journal.pcbi.1002202
>
>
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