Hi,
On 16 Oct 2007, at 12:58, Matt Glasser wrote:
> Hi Steve,
>
> Well okay, but why would the ROIs line up with FSL's standard brain in
> MRIcro, but not in FSL itself? I used the same standard space
> image in both
> programs
Ah - I hadn't appreciated that - sorry...
> and it was only misaligned in one of them, so I don't know how I
> could use a flirt transform in this case.
Right - in that case the difference presumably is because MRICRO uses
the co-ordinate centre from the header in determining display
centering, whereas FSLView only uses the raw voxels for working out
display (the co-ordinate centre is only used in the reporting of the
mm co-ordinates, not in the image display).
Cheers, Steve.
>
> Thanks,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Steve Smith
> Sent: Tuesday, October 16, 2007 2:00 AM
> To: [log in to unmask]
> Subject: Re: [FSL] MNI Space in MRIcro and FSL
>
> 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.
>>
>>
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
------------------------------------------------------------------------
---
|