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Bug 3435 - Syntax error using vol2mesh

Reported 2018-07-02 21:27:00 +0200
Modified 2019-08-10 12:37:18 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Linux
Importance: P5 normal
Assigned to:
Depends on:
See also:

Jiaming - 2018-07-02 21:27:27 +0200

Line 73 of prepare_mesh_tetrahedral.m It seems that the code tries to feed an isovalue (which is defined in Line 72) to vol2mesh. If my understanding is correct, the use of vol2mesh [node, elem, face] = vol2mesh(seg, 1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 2, 2, isovalue); is incorrect, according to the documentation fo vol2mesh. I'd suggest changing the line to: [node, elem, face] = vol2mesh(seg, 1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 2, 2,1,'cgalsurf', isovalue);

Jan-Mathijs Schoffelen - 2018-11-21 15:30:56 +0100

Hi Simon, could you look into this? Thanks, JM

Simon - 2018-11-21 17:23:12 +0100

So investigated prepare_mesh_tetrahedral line 72. Indeed i found an incorrect usage of vol2mesh. It is used as followed: isovalue = 0.5; [node, elem, face] = vol2mesh(seg, 1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3), 2, 2, isovalue); However, looking into vol2mesh i found this usage: vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues) According to the code we parsed the value 0.5 into dofix, and method and isovalues is left empty. However, dofix is a binary. So I looked into vol2mesh. In line 60 an IF starts. Here is were the incorrect usage of vol2mesh is dealt with, with nargin=7 we end in line 65. So I propose to change line 72, to make the behaviour more explicit, and consistent with the documentation. This will not change the output of prepare_mesh_tetrahedral. Pull request is coming!

Jan-Mathijs Schoffelen - 2018-11-22 17:06:48 +0100

Thanks Simon! I have approved the PR, will close this for now. Jiaming feel free to reopen if the problem persists.

Robert Oostenveld - 2019-08-10 12:37:18 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on