I have not noticed this on Ubuntu 12.04. Do all the other FSL tools work?
Do you have the auxiliary FSL packages installed (like the FSL atlases)?
Peace,
Matt.
On 5/14/14, 8:31 AM, "Matyá¹" <[log in to unmask]> wrote:
>Hi,
>
>There is no error message from fslreorient2std, but there is no output
>either (I tried to call it alone like this: fslreorient2std T1.nii - and
>there was no output to terminal). The thing with convert_xfm is that in
>fsl_anat script it first run fslreorient2std, this should provide
>T1_std2orig.mat (or I think it should), and this is input for
>convert_xfm in the fsl_anat pipeline (convert_xfm -omat T1_std2orig.mat
>-inverse T1_orig2std.mat) - and this ends with "Cannot read
>input-matrix" error.
>
>I installed it with Neurodebian as you said, but I has version 4.1. also
>installed on my PC, so maybe this could do some problems.
>
>
>
>
>Dne 14.5.2014 15:17, Mark Jenkinson napsal(a):
>> Hi,
>>
>> I have not heard of this before, and it is very concerning.
>> How does the convert_xfm error relate to fslreorient2std (as the latter
>>does not call convert_xfm)?
>>
>> If you just run fslreorient2std on its own, do you get an error message?
>>
>> And did you install FSL via NeuroDebian, or some other way?
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 14 May 2014, at 15:02, Matyá¹ <[log in to unmask]> wrote:
>>
>>> Hi all,
>>>
>>> I want to ask if anyone has experienced that fslreorient2std doesn't
>>>provide any output in Ubuntu 12.04 or above (I'm using fsl 5.0.6). I
>>>wanted to try fsl_anat script for my structural data, but in first step
>>>of this script it exits with error message that convert_xfm could not
>>>read T1_std2orig.mat and after while I found out that this is problem
>>>of fslreorient2std. It does the same on my laptop with Ubuntu 14.04.
>>>Any idea why this is happening?
>>>
>>> Thank you,
>>>
>>> Matyas
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