Hi
display itself is an ImageMagick tool that comes with fsl and can
display gifs jpegs and such - it cannot read or display raw avws. If you
want a lightbox view of a single 3d avw image, you can use display in
combination with slicer, e.g.
$ slicer structural -A 800 grot
$ display grot
should show you all slices in a single image (800 pixels wide). The file
grot is a simple PGM graphic file that can be displayed using a wide
range of image display/manipulation software (like gimp or display)
Using convert (also part of ImageMagick) you can turn that file into
whatever you fancy
$ display grot
or
$ convert grot grot.gif
$ open /Application/Preview.app grot.gif
should work beautifully on your mac :)
ta
Christian
Goldfine, Andrew (NINDS) wrote:
> I just ended up flipping the structurals with ImageJ on my Mac which worked
> fine.
>
> I've tried AFNI for visual display and it seems pretty easy.
>
> With display I tried opening .hdr or .img files that FSL had no trouble
> using and it said it was an invalid format.
>
> Thanks
>
> -----Original Message-----
> From: Christian Beckmann [mailto:[log in to unmask]]
> Sent: Saturday, July 13, 2002 8:37 AM
> To: [log in to unmask]
> Subject: Re: [FSL] image flipping
>
> Hi
>
> within FSL you'd normally use flirt to do this kind of thing. All you need
> is to create a 4x4 matrix in a text file and pass this to flirt with the
> -init -applyxfm option. An example would be
>
> 1 0 0 0
> 0 -1 0 (FOV Y)
> 0 0 1 0
> 0 0 0 1
>
> if you want to flip around y. Mark Jenkinson has explained this in more
> detail in an email to the fsl list on the 21. Nov 2001
>
> WRT your second question: FSL does not yet come with an interactive
> display utility. For this kind of thing, we recommend tools like Krish
> Singh's mri3dX, mricro, 3D visionworks, MEDx etc
> Within fsl, the three tools available are
> slices, which gives you a 3x3 array of views : try slices example
> slicer, which creates a graphics file that can then be viewed using
> display
> overlay, which allows you to overlay one image onto another
>
> I'm surprised that display does not seem to work for you, how are you
> using it?
>
> ta
> Christian
>
>
> Christian F. Beckmann
> Address: Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7980 691852
>
> On Sat, 13 Jul 2002, Darren Weber wrote:
>
>
>>Hi Andy,
>>
>>what is the slice orientation of the analyze files - axial, sagittal,
>>coronal? Which of these orientations is the y direction?
>>
>>The default Analyze volume is radiological orientation, that is +XYZ = RAS
>>(right, anterior, superior).
>>
>>Maybe you can use AIR to flip the volumes, just in Y.
>>
>>If you use mricro and AIR, you could evaluate the orientation problem for
>>one EPI volume and then develop a script to apply it to all of them.
>>
>>Kind regards, Darren
>>
>>PS, My apologies to the FSL team for butting in. You can probably do this
>>stuff with avwutils?
>>
>>
>>----- Original Message -----
>>From: "Andy Goldfine" <[log in to unmask]>
>>To: <[log in to unmask]>
>>Sent: Saturday, July 13, 2002 6:21 AM
>>Subject: [FSL] image flipping
>>
>>
>>
>>>My EPI images (from GE then converted to ANALYZE and then a hdr created
>>>with avwcreatehd) have the y orientation backwards making registration
>>>impossible. Is there a way to flip the y axis of images?
>>>
>>>Secondly, FSL is missing an image display utility like in SPM. How do
>>>you recommend displaying images to see how they look and also to do
>>>orientation. "display" doesn't seem to work and "slicer" seems
>>>difficult.
>>>
>>>Thanks
>>>
>>
>
>
--
Christian F. Beckmann
Address: Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7980 691852
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