[Mrtrix-discussion] Converting mif TDI images into nii

[Marta Correia]

Dear Gavin,

Thanks for your reply. I was using 4.1.9 and after I used fslchfiletype on the TDI file I was then able to open it with fslview. However that has made me notice that the converted nii only has zeros in it, even when loaded in MRview. Any ideas of what could have gone wrong with the conversion.

Thanks again,

Marta


-----Original Message-----
From: mrtrix-discussion-bounces at www.nitrc.org [mailto:mrtrix-discussion-bounces at www.nitrc.org] On Behalf Of Gavin Winston
Sent: 05 October 2012 09:39
To: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] Converting mif TDI images into nii

On 05/10/12 09:31, Marta Correia wrote:
> Dear MRTrix,
>
>
>   I was wondering whether the issue described in the email from 16^th of
>   June with the subject 'Converting Fraction Images to Nifti' was ever
>   resolved. I have exactly the same problem (same error message in
>   fslview, etc) so it would be very useful to know whether you ever
>   found the answer.
>
> To sum up the problem, when I try to convert a mif file generated with tracks2prob into nii by using the command mrconvert input.mif-datatype int16 output.nii the generated nii file cannot be opened with fslview and I get the following error message in the terminal:
>
>
>
> /fslview: line 6: 2206 Segmentation fault ${FSLDIR}/bin/fslview_bin 
> $@/
>
>
>   Many thanks in advance,
>
>
>   Marta

Dear Marta,

I get this error message with FSLview in FSL version 4.1.9 for many images not just those generated by MRtrix.  It appears there is a bug in FSL where it is trying to write to the file system in which it is installed (which is read-only in my case).

This error does not occur with FSL 4.1.7 or FSL 5.0.0/5.0.1.  Which version are you using?

Gavin

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