HI - I presume this is because of a change in field-of-view in the
different standard space images. One easy way to solve that is to use
flirt to estimate the transform between the standard space image in
SPM/mricro and the FSL standard space image, and use that instead of
eye.mat in your call to flirt resample the ROI.
Cheers, Steve.
On 16 Oct 2007, at 00:17, Matt Glasser wrote:
> Hi,
>
>
>
> I have a set of ROIs from SPM in MNI space that I want to load into
> FSL. When I take the standard FSL brain MNI152_T1_1mm_brain and
> load it in MRIcro and overlay the ROI, it looks fine, like the
> first screenshot: http://www.ma-tea.com/~Matt/MRIcroOnMNI.png
> However, if I resample the 4X4X4mm ROI so it can be overlayed on
> this brain in FSLView, using:
>
>
>
> flirt –in 4X4X4mmROI –ref MNI152_T1_1mm_brain –applyxfm –init
> eye.mat –out 1X1X1mmROI where eye.mat is the identity matrix:
>
>
>
> 1 0 0 0
>
> 0 1 0 0
>
> 0 0 1 0
>
> 0 0 0 1
>
>
>
> The result is incorrect, shown by the second screenshot in FSLView:
> http://www.ma-tea.com/~Matt/FSLOnMNI.png
>
>
>
> The ROI file header is the following:
>
>
>
> <nifti_image
>
> nifti_type = 'ANALYZE-7.5'
>
> image_offset = '0'
>
> ndim = '4'
>
> nx = '41'
>
> ny = '48'
>
> nz = '35'
>
> nt = '1'
>
> dx = '4'
>
> dy = '4'
>
> dz = '4'
>
> dt = '1'
>
> datatype = '16'
>
> nbyper = '4'
>
> byteorder = 'LSB_FIRST'
>
> cal_min = '0'
>
> cal_max = '1'
>
> descrip = 'FSL4.0'
>
> sform_code = '2'
>
> sto_xyz_matrix = '-4 0 0 80 0 4 0 -112 0 0 4 -52 0 0 0 1'
>
> num_ext = '0'
>
> />
>
>
>
> I would appreciate any assistance with this as I am unfamiliar with
> this type of issue if it has to do with the analyze file format or
> header.
>
>
>
> Thanks,
>
>
>
> Matt.
>
>
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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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