Thank you!
I will check this out.
Best,
Aga
On 26.01.2008 8:35 Uhr, "Steve Smith" <[log in to unmask]> wrote:
> Hi,
>
> Ah, I think I know what's happening now. It sounds like you are
> getting wrapping from very large numbers round to being negative as
> the scaling being applied in the script is too large. Please see the
> TBSS manual where it is described how to set the scaling factor as an
> argument to tbss_1_preproc so that the preprocessed data ends up with
> range mostly 0:10000. If you have done this correctly for most voxels
> but still have a few high intensity outliers then you could just hard
> limit those before running tbss_1_preproc with the -min option in
> fslmaths.
>
> Cheers.
>
>
> On 25 Jan 2008, at 18:30, Agnieszka Burzynska wrote:
>
>> Hi,
>> Thank you! I applied one more time fslstats to my images. Indeed, the
>> location of the negative voxels may not be too problematic, but the
>> negative
>> values are of the same range as positive (eg. -31688 and 30531, I
>> did not
>> divide by 3 to get it closer to 10000) and on the origdata histogram
>> I see
>> really nothing below zero, too.
>> I just wonder if I did any basic mistake or something else could have
>> happened.
>>
>> Best wishes,
>> Aga
>>
>>
>> On 25.01.2008 17:47 Uhr, "Steve Smith" <[log in to unmask]> wrote:
>>
>>> Hi,
>>>
>>> I don't think that tbss_1_preproc (at least the version with FSL4)
>>> can
>>> create new negative values, but it does multiply the original values
>>> to make them a lot larger, so maybe you started with VERY slightly
>>> negative values that are sufficiently small that you didn't notice
>>> them, and after the rescaling, they were more obvious? It's probably
>>> not a problem anyway if they are around the edge of the brain?
>>>
>>> Cheers, Steve.
>>>
>>>
>>>
>>> On 25 Jan 2008, at 10:36, Agnieszka Burzynska wrote:
>>>
>>>> Dear all, I resend this message, because I still do not know what is
>>>> wrong:
>>>>
>>>>
>>>> Hi,
>>>> I applied tbss_1_preproc to my S0 images. In origdata, none of them
>>>> had
>>>> values below 0, however, after the scaling in the FAi folder there
>>>> are 2
>>>> cases, in which I see negative values around the brainstem.
>>>>
>>>> How did this happen and what should I do? I thought it is just a
>>>> simple
>>>> mulitiplication by a given number (here by 10).
>>>>
>>>> Thank you and best wishes,
>>>> Aga
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> ---------------------------------------------------------------------------
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
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