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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