[FieldTrip] Problem reading .mgz files

[jan-mathijs schoffelen]

Yes, please use linux. Lines 61-76 in read_mgh (which is in ~/fieldtrip/external/freesurfer) suggest that files with extension .mgz can only be read with linux or MacOS.

BW,

JM

Line 

On Jan 13, 2012, at 11:07 AM, Ion Lavado wrote:

> Ok, i'm using Windows platform and Linux for generating the freesurfer mri (.mgz) files. So do you think the solution would be running the matlab script with Linux? Or what can i do to change the style path?
> 
> Best wishes,
> 
> Ion
> 
> 2012/1/13 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> Hi Ion,
> 
> What operating system are you working on? It looks like windows, and the first error is a path error, where the function is looking at a Linux-style path.
> 
> This is apparently causing trouble. First you get two errors (starting with ERROR, which are a sign that something went wrong in the low level reading routines), which do not cause matlab to 'crash' directly. Later in the code variables are not what they are expected to be (due to the earlier ERRORs) and this causes a matlab crash (in red).
> 
> So far this whole pipeline has been tested only on the linux platform. I don't know whether freesurfer (in particular the matlab functions that FieldTrip relies on to read in the .mgz files) runs without problems on windows. 
> Perhaps you first need to find out what causes the first error. It could well be that FieldTrip needs to use a platform specific reading routine here.
> 
> BW,
> 
> JM
> 
> 
> 
>  
> On Jan 13, 2012, at 10:00 AM, Ion Lavado wrote:
> 
>> Hello, i'm trying source reconstruction using Minimum-Norm Estimates and i have a problem when reading the (filled.mgz) or any other .mgz file after using Freesurfer and created the files.
>> This is the ERROR i get:
>> 
>> 
>> >> mri=ft_read_mri('F:\SUBJECT29_BUENO\Subject29\mri\filled.mgz');
>> The system cannot find the path specified. 
>> ERROR: could not open /tmp/tmp7914012.mgh for reading
>> ERROR: loading F:\SUBJECT29_BUENO\Subject29\mri\filled.mgz as MGH
>> ??? Attempt to reference field of non-structure array.
>> Error in ==> ft_read_mri at 248
>>   ndims = numel(size(tmp.vol));
>> 
>> Hope anyone can help me. Thanks!
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> Jan-Mathijs Schoffelen, MD PhD 
> 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> 
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
> 
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
> 
> 
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> _______________________________________________
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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