I would work out first if you actually need this; check whether the
initial alignments from FIRST are reasonable?
Cheers.
On 24 Feb 2009, at 01:07, Nestor, Liam (Contractor) wrote:
> Hi Brian
>
> Thanks for the reply. How does one pre-align (e.g., ac-pc) in FSL? I
> have been searching for this but to no avail.
>
> Thanks,
>
> Liam.
>
>
> *******************************************
> Liam Nestor, Ph.D
> Office C8-523
> Laboratory for Molecular Neuroimaging
> Semel Institute for Neuroscience and Human Behavior
> 760 Westwood Plaza
> Los Angeles 90024
> Tel: 310-206-0655
> E-mail: [log in to unmask]
> *******************************************
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
> Of Brian Patenaude [[log in to unmask]]
> Sent: Monday, February 23, 2009 12:06 PM
> To: [log in to unmask]
> Subject: Re: [FSL] T1-weighted images and segmentation
>
> Hi,
>
> Just to clarify, the subcortical mask is only used at the second
> stage.
> The first stage is a 12 dof registration using FLIRT (includes the
> skull).
>
> If you do pre-align the image using a linear transform prior to
> first_flirt, you could save the transform, then multiply it with the
> output from first_flirt (using convert_xfm). By doing this the model
> will
> be transformed into the native space prior to any interpolation.
>
> Cheers,
>
> Brian
>
>
>> Is it possible to do a ac-pc realigment in FSL. I am not referring
>> to the
>> normalization process. I just want to realign the T1-weighted
>> images. By
>> doing this, might I improve the integrity of the segmentation
>> process?
>>
>> Liam.
>>
>>
>> *******************************************
>> Liam Nestor, Ph.D
>> Office C8-523
>> Laboratory for Molecular Neuroimaging
>> Semel Institute for Neuroscience and Human Behavior
>> 760 Westwood Plaza
>> Los Angeles 90024
>> Tel: 310-206-0655
>> E-mail: [log in to unmask]
>> *******************************************
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of
>> Steve Smith [[log in to unmask]]
>> Sent: Saturday, February 21, 2009 8:40 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] T1-weighted images and segmentation
>>
>> Hi, yes it is worth getting the first stage of the FIRST scripts (the
>> standard space registration) working accyurately, though note that
>> this uses a subcortical mask to optimize registration in the
>> subcortical area, so may not look globally otimal. Cheers
>>
>> --------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington,
>> Oxford. OX3 9 DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask]
>> http://www.fmrib.ox.ac.uk/~steve
>> ----------------------
>>
>> On 20 Feb 2009, at 18:15, Liam Nestor <[log in to unmask]>
>> wrote:
>>
>>> Hello there FSL people.
>>>
>>> I am new to FSL First. I am currently using first_flirt and
>>> run_first to
>>> perform alignment and segmentation of subcortical structures, which
>>> I then
>>> compute the volume of (nonzero voxels) using fls_stats.
>>>
>>> I have scripted this whole process and everything seems to be
>>> working very
>>> well. I have noticed, however, some of my T1-weighted images in
>>> native space
>>> are not particularly straight (i.e. a bit twisted - not well
>>> aligned). I
>>> understand that we transfer our image in native space to 152MNI, but
>>> segmentation actually takes place on the image in native space.
>>>
>>> My main question is whether images not well aligned in native space
>>> are
>>> likely to have an effect on the integrity of the segmentation
>>> process? If it
>>> is, does FSL have a programme to straighten up the images in native
>>> space.
>>>
>>> Many Thanks,
>>>
>>> Liam.
>>>
>>>
>>
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---------------------------------------------------------------------------
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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