Hi,

This sounds bad - I suspect your file is corrupted.
Does it look OK in FSLView?
If it looks OK and you cannot get fsl_motion_outliers to work
then send us the data via:
    http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
(and email us the reference number) and we
will see if we can figure out the problem here.

All the best,
Mark


On 6 Oct 2009, at 12:23, Daniel Shaw wrote:

> Hi all,
>
> It seems the issue I'm having might be due to the size of my images.
> The command works fine when using a colleague's 40MB files, but not
> when using my 90MB files. I also notice that I get a "nifti bufffer"
> error message when the images are read in. If this is the case, how
> can overcome this issue?
>
> Thanks in advance,
>
> Dan.
>
> On Oct 5, 2009, at 3:31 PM, Daniel Shaw wrote:
>
>> Hi,
>>
>> Following from my previous post (below), it seems that the
>> fsl_<tmp_folder>_mc/stp file is not created, possibly because my
>> $val is 0. I'm afraid this is as much as I can get from the
>> fsl_motion_outliers script, but this might help someone diagnose
>> the problem.
>>
>> Again, any help would be greatly appreciated.
>>
>> Regards,
>>
>> Dan.
>>
>>
>> On Oct 5, 2009, at 2:23 PM, Daniel Shaw wrote:
>>
>>> Dear all,
>>>
>>> I'm having issues with fsl_motion_outliers. Specifically, no
>>> confound file is generated. The
>>> problem may start before the output file written, as indicted by
>>> the feedback I get (an
>>> example is provided below):
>>>
>>> fsl_motion_outliers <input.nii.gz> 0 <output.txt>
>>>
>>> Generating residual mean square error
>>> Calculating outliers
>>> Found 17 outliers over 7.43853
>>> Generating EVs
>>> Found spikes at
>>>
>>> That is, no further information is provided regarding the spikes
>>> found.
>>>
>>> Having searched the archived I have tried converting from
>>> "neurological" to "radiological"
>>> orientation using fslswapdim and fslorient, but still no confound
>>> found is generated.
>>>
>>> Can anyone tell me where I might be going wrong or what I might
>>> try next? Any advice
>>> would be extremely helpful.
>>>
>>> Many thanks in advance,
>>>
>>> Dan.
>>
>> Daniel Shaw M.Sc.
>> PhD student
>> Brain & Body Centre
>> University of Nottingham
>> University Park
>> Nottingham
>> NG7 2RD
>>
>>
>>
>>
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>>
>
> Daniel Shaw M.Sc.
> PhD student
> Brain & Body Centre
> University of Nottingham
> University Park
> Nottingham
> NG7 2RD
>
>
>
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses, which could damage
> your computer system: you are advised to perform your own checks.
> Email communications with the University of Nottingham may be
> monitored as permitted by UK legislation.
>