Hi Tom,
The reason you did not see your datasets in the file menu is that they are
not in an accepted file format.
Do you have access to matlab? If you do, I suspect the easiest way to
create analyze or nifti format files from your .bmp files, is to load
them into matlab, stack them into a 3D array, and save them using
save_avw ( you can find this function in $FSLDIR/etc/matlab ).
If you don't have access, there are other converters that can write
analyze files. For a list of such converters, see
www.psychology.nottingham.ac.uk/staff/cr1/mricro.html#otherconv
Then you should be good to go.
Hope this helps
Tim
On Tue, 3 May 2005, Tom Al wrote:
> Hi Gio,
>
> Thanks very much for your reply. It sounds like Flirt may be useful for me
> although I am sure that I have a fairly steep learning curve ahead of me.
>
> My data sets are contiguous.
>
> The raw data is in the form of a series of 2d bitmaps and they can be
> stacked together to generate the 3d dataset.
>
> The tomography reconstruction generates *.bmp files but I know how to do a
> conversion to ANALYZE format. What input is required? Is it a stacked
> image file in ANALYZE format?
>
> I believe that a rigid body registration will be perfect for my application
> if it is capable of 3-axis translations and 3 rotation axes. This is
> available in Flirt, is it not?
>
> I downloaded the FSL software and followed the instructions to set up and
> run under cygwin. I then ran the FSL Evaluation and Example Datasuite
> (FEEDS) v3.2. The FEEDS run was successful with all tests passed. However,
> when I tried to load a dataset in FLIRT, using the open file menu, the file
> name did not register in the I/O menu when I clicked on them. I have to
> solve this problem before I can go further and try one of my datasets. I
> appreciate your offer to address some of my questions. I promise not to
> abuse your good will. I may then be incontact with you after I get this
> file I/O issue solved.
>
> Best regards.
>
> Tom
>
> ----- Original Message -----
> From: "Gio Buonaccorsi" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Tuesday, May 03, 2005 10:12 AM
> Subject: Re: [FSL] Registration of time-series CT datasets
>
>
> Hi Tom,
>
> I don't know if you've had an off-list reply but I'll have a go at this
> based on extensive use of flirt.
>
> Flirt uses voxel-intensity-based similarity measures and works in "real
> space" (i.e. it converts voxel co-ordinates to mm space based on the
> voxel dimensions and an offset position included in the image headers).
> So in theory it should be able to work with any grayscale data in a
> supported image format.
>
> I know flirt will work with NIFTI and Analyze format images (I've only
> used the latter myself), so if your data is in either of these formats,
> or can easily be converted, you have a better chance it will work.
>
> There are a couple of things I don't know, though, that may cause
> problems. All of my data is MR volume data with contiguous slices. If
> you have slice gaps or interleaving I don't know if flirt will be happy
> with that. I expect the registration algorithm will deal happily with
> the data but will interpolate maybe to voxel positions for which your
> original data sets don't have data. I'm not sure how meaningful this
> will be - I guess you'll have a better idea of that, and you might have
> contiguous data anyway.
>
> I also don't know enough in general about your data to know if the
> registration transformations are suitable. Flirt applies affine
> transformations (i.e translation, rotation, scale and shear) which from
> a naive viewpoint I assume would be suitable for rock samples. But if
> you have any non-linear or warping deformations flirt can only give you
> the best affine approximation to the real deformation.
>
> I'd guess if your data is in the right format it's worth having a try.
> Although flirt was designed for use with brain data, where affine
> transforms are usually a good approximation to real motion, we've had
> great success applying it to abdominal data sets with complex motion, by
> using appropriate weighting masks.
>
> I hope this helps. Please feel free to get in touch again if you have
> any more questions.
>
> Gio Buonaccorsi
> ISBE
> University of Manchester
> [log in to unmask]
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Tom Al
> Sent: 29 April 2005 20:35
> To: [log in to unmask]
> Subject: [FSL] Registration of time-series CT datasets
>
> Hi there,
>
> I am collecting CT image sets of a rock volume sequentially through
> time. I need to register the volume of all datasets against the first
> data. I understand that FSL/FLIRT is intended for MRI datasets but is
> it possible to use it for my purpose, with stacks of grey-scale bitmap
> images?
>
> Tom A. Al
> Associate Professor
> Department of Geology
> University of New Brunswick
> P.O. Box 4400
> Fredericton, NB, Canada
> E3B 5A3
> Ph: 506-447-3189
> fax: 506-453-5055
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
|
