Hi,
You should just feed the _original_ images into SIENA; as long as they
are in the same rough orientation and using the same MRI acquisition,
no further pre-processing should be necessary. You should only
potentially adjust the orientation using fslswapdim, which doesn't
interpolate the images, just swaps the axes around if necessary - no
more than that. SIENA will take care of the alignments for you; see
the SIENA manual page for more details.
Cheers, Steve.
On 12 Feb 2008, at 10:10, Shireen, Kwiatkowska wrote:
> Hi, I already have structural data (two time points for every
> subject), which I want to analyse. These were already aligned for
> other purposes, but this was done "per hand" and is rather
> approximative. As I tought Siena does align the two brains to each
> other using the skull, I did not think the actual previous position
> of the brains would be an issue. But then different aliging of the
> same brains gave me different results. So now I would like to know,
> what the preprocessing steps should be, before I apply siena to
> detect brain volume chage that took place between the two time points.
>
> Greetings,
>
> Shireen
>
> -----Wiadomość oryginalna-----
> Od: FSL - FMRIB's Software Library w imieniu Steve Smith
> Wysłano: Wt 2008-02-12 10:34
> Do: [log in to unmask]
> Temat: Re: [FSL] ODP: [FSL] Siena and alignment
>
> Hi - I'm not sure if you are talking about issues relating to data
> acquisition or data analysis?
> Steve.
>
> On 12 Feb 2008, at 08:27, Shireen, Kwiatkowska wrote:
>
>> Hi,
>>
>> would then co-registering the two brains in Flirt, using one of them
>> as a reference be the appropriate method to acquire perfectly
>> aligned brains?
>>
>> Cheers,
>>
>> Shireen
>>
>>
>> -----Wiadomość oryginalna-----
>> Od: FSL - FMRIB's Software Library w imieniu Steve Smith
>> Wysłano: N 2008-02-10 17:30
>> Do: [log in to unmask]
>> Temat: Re: [FSL] Siena and allignment
>>
>> Hi, SIENA is all about comparing the same brain from two different
>> timepoints after they have been aligned to each other as well as
>> possible. So yes, different alignments between the two images are
>> very
>> likely to affect the output.
>>
>> Cheers.
>>
>>
>> On 9 Feb 2008, at 14:50, Shireen, Kwiatkowska wrote:
>>
>>> Hello!
>>>
>>> I would like to know how does allignment influence Siena results. I
>>> have run Siena with the use of the -m option on differently alligned
>>> brains (all other parameters constant) and have obtained slightly
>>> different results. Could someone briefly explain why?
>>>
>>> Cheers,
>>>
>>> Shireen
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library on behalf of Jessica Kirkland
>>> Sent: Fri 2/8/2008 10:24 PM
>>> To: [log in to unmask]
>>> Subject: [FSL] Modeling a motor response
>>>
>>> Hi everyone,
>>>
>>> I am interested in modeling a button-press response, primarily to
>>> check for
>>> associated motor activation in several subjects who have data that
>>> looks
>>> somewhat sketchy. I'm wondering if anyone has done this, and if you
>>> have
>>> recommendations about how to model this for a quick and dirty
>>> analysis. I am
>>> unsure of the duration I should use to allow for modeling the motor
>>> response. Thank you in advance for the advice!
>>>
>>> Jessica
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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