open-discussion > Create gifti surfaces from lh.white for MATLA
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May 24, 2014  01:05 AM | Bastian Cheng
Create gifti surfaces from lh.white for MATLA
Dear gifti-experts,
 
I would like to create gifti-surfaces to use in matlab.

That's what I am doing so far:
mris_convert lh.white lh.white.gii

I then try to open it using the "gifti" command


however, I get an error message from matlab:
 
>>>>>>>>>>>
??? Attempt to reference field of non-structure array.
Error in ==> gifti.subsref at 28
varargout{1} = this.data{j}.space.MatrixData;
Error in ==> gifti.struct at 17
[values{i,:}] = subsref(this(:), substruct('.',names{i}));
Error in ==> gifti.display at 17
eval([display_name ' = struct(this);']);
>>>>>>>>>>>>>>>

I am using the current version of FS. v5.3.0
 
Am I missing something? Is there anything special with the .gii file form FS?
Any help is appreciated!
May 24, 2014  06:05 AM | Nick Schmansky
Create gifti surfaces from lh.white for MATLA
Bastian,

I have not tested the freesurfer gifti output in matlab. What command are you using in matlab to open the file? Are you able to open your lh.white.gii file in another program that supports gifti? (in freesurfer, to test file validity, you can load it with: freeview -f lh.white.gii) also, another option is to use the matlab command �read_surf.m�, found in your freesurfer/matlab directory, to load the lh.white file in matlab.

Nick



May 25, 2014  06:05 AM | Bastian Cheng
RE: Create gifti surfaces from lh.white for MATLA
Hi Nick,
 
Thank you very much for your reply!
Yes, I have opened the gifti file with freeview successfully.
In matlab, I am using the command:
g=gifti('filename')
with the error message shown before.
I have attached my file that was converted from FS using mri_s:
Also, I have posted a question on the FS support site, but had no reply so far.
Maybe you could have a look at the file. It seems little different
from the template provided at the gifti toolbox homepage.
Best,

Bastian
May 25, 2014  07:05 AM | Bastian Cheng
RE: Create gifti surfaces for matlab
Hi Nick,
 
Thank you very much for your reply!
Yes, I have opened the gifti file with freeview successfully.
In matlab, I am using the command:
g=gifti('filename')
with the error message shown before.
I have attached my file that was converted from FS using mri_s:
Also, I have posted a question on the FS support site, but had no reply so far.
Maybe you could have a look at the file. It seems little different
from the template provided at the gifti toolbox homepage.
Best,

Bastian
May 29, 2014  04:05 AM | Nick Schmansky
Create gifti surfaces for matlab
Bastian,

Hi, I've posted a new mris_convert which should solve the problem for
you. It's built for Centos 6, so if you need it for another platform,
let me know. It's here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dis...

Nick

Oct 25, 2016  05:10 AM | Rogier Mars - University of Oxford, Department of Experimental Psychology
RE: Create gifti surfaces for matlab
Dear Nick,

Is this version available for Mac (Yosemite) as well?

Thanks very much,

Rogier
Oct 25, 2016  07:10 AM | Nick Schmansky
RE: Create gifti surfaces for matlab
Hi,

You will need to download the 'development' version of the entire freesurfer package in order to get the binary mris_convert.  Note that is version is pre-version 6 release, which we hope to release within a month.

ftp://surfer.nmr.mgh.harvard.edu/pub/dis...

Nick