PS:
Just to clarify - setting the 4th dimension to be 3 (if there is a
single image) won't
give you something that makes sense in FSLView or other programs.
You would
definitely need to do a funky reordering (e.g. in MATLAB) to produce
something
that looks correct. You could also do the reordering in FSL using a
script it to split up
the individual channels using avwroi and avwcreatehd, by making
dim1=3, dim2=Nx*Ny,
dim3=Nz, dim4=Nt initially, then splitting into three images
(splitting the x dimension)
and then replacing the headers with new headers that have the
standard sizes
(dim1=Nx, dim2=Ny, dim3=Nz, dim4=Nt).
On 29 May 2007, at 08:56, Mark Jenkinson wrote:
> Hi,
>
> I'm afraid that FSL has never supported RGB and is unlikely to -
> sorry.
> As this type stores three 8-bit values per voxel, that will also
> make it very
> difficult to convert to another type. The easiest way is probably
> to write
> a header where the 4th dimension is 3 (or 3 * number of time
> points) and
> the datatype is 8-bit (datatype 2). This would then allow it to be
> read in, but
> would require reshaping to get into another form if that's what you
> want,
> which could be done using matlab.
>
> Hope this helps in some way.
> All the best,
> Mark
>
>
> David Chang wrote:
>
>> Hi,
>>
>> Thanks for the response. I think datatype 128 is type ARGB. I have
>> no problem viewing this analyze file using other image application
>> but due to the way we're processing our batch images (CATNAP have
>> no support for analyze format file currently), the quickest way is
>> to generate the header file and flip the image through linux bash
>> script.
>>
>> Thanks, Dave
>>
>> On 5/29/07, *Steve Smith* <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>> Hi - this sounds like an invalid Analyze datatype maybe. Why not
>> persuade CATNAP to output it as a different datatype?
>> Cheers.
>>
>>
>> On 29 May 2007, at 03:12, David Johnston wrote:
>>
>> > Hi
>> >
>> > I am running into some problem flipping images using
>> avwswapdim.
>> > We're using
>> > CATNAP DTI to create fa, adc and cmap images. We than use
>> > avwcreatehd to
>> > convert these images to analyze format, but during this
>> conversion,
>> > the y
>> > orientation is set to opposite for some reason. We than use
>> > avwswapdim to
>> > re-orientate these images. fa and adc images (datatype =14)
>> works
>> > perfectly
>> > but for cmap (datatype=128), avwswapdim complains about no-
>> support
>> > for this
>> > particular datatype. Is there another way to flip datatype
>> 128 ?
>> >
>> > Thanks, Dave
>>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---
>> 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]
>> <mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
>> <http://www.fmrib.ox.ac.uk/%7Esteve>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---
>>
>>
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