Hi - no, you can use the standard images as supplied. We didn't yet
convert them because we knew that they were working fine (with input
data of either type)!
Cheers, Steve.
On 1 Jun 2006, at 18:57, Jeffrey Spielberg wrote:
> Hi, we have noticed that the MNI standard brain that came with FSL
> 3.3 (i.e. avg152T1_brain) is in Analyze format. Will this cause an
> origin problem during our Feat analyses? Since our input files
> would be in nifti format to counter the origin problem, should we
> use an avg152T1_brain in nifti format, and is there one available?
> Or should we convert the analyze format brain that comes with the
> package to nifti oursleves? Thanks,
> Jeff
>
> On 5/24/06, Mark Jenkinson <[log in to unmask]> wrote: Hi,
>
> Yes, it seems that a minority of machines are experiencing
> problems with Analyze files and non-zero origins, probably
> due to some library differences with some of our C calls (as
> the C++ code doesn't seem to be affected).
>
> Our recommended solution is to use the nifti format.
>
> If you must have Analyze to pass onto other programs, then
> convert the nifti format to Analyze after all the FSL processing
> is done by using avwchfiletype. This solution has worked for
> other users and so hopefully this will solve your problems.
>
> All the best,
> Mark
>
>
>
>
> On 24 May 2006, at 18:39, Jeffrey Spielberg wrote:
>
> > Hi, we have discovered that using avwmaths produces this change in
> > "mm" values as well. Is this something that we need to worry about
> > happening in Feat as well? We have also found that using bet2 does
> > not produce the same weird change in "mm" values, but it does set
> > the x value for pixel size to a negative value ( i.e. pixdim1 =
> > -3.4375 where before it had been positive). Will this produce a
> > problem later in Feat? Thanks,
> > Jeff
> >
> > On 5/16/06, Mark Jenkinson < [log in to unmask]> wrote:Dear Jeff,
> >
> > I'm having a lot of trouble reading your open office format.
> > Could you please resend as plain text.
> >
> > All the best,
> > Mark
> >
> >
> > On 16 May 2006, at 20:09, Jeffrey Spielberg wrote:
> >
> > > Hi, we are also having this problem after using bet. I am
> > attaching a
> > > document with the details for our system that you asked Matt
> for, in
> > > the hope that this can help you track down the problem, thanks,
> > > Jeff
> > >
> > > On 5/15/06, Mark Jenkinson < [log in to unmask]> wrote:
> > >> Dear Matt,
> > >>
> > >> I cannot replicate this problem at our end with any combination
> > >> of Analyze or Nifti.
> > >>
> > >> Could you please let me know the following details:
> > >> - your platform
> > >> - the version of FSL you are using
> > >> - the avwhd output of the input and output images
> > >> - the exact commands that you are running
> > >>
> > >> Hopefully this will let us track it down.
> > >> All the best,
> > >> Mark
> > >>
> > >>
> > >>
> > >> On 15 May 2006, at 19:31, Matt Holloway wrote:
> > >>
> > >> > Hi,
> > >> >
> > >> > I'm trying to brain extract and noise-reduce a set of T1
> > structural
> > >> > images
> > >> > to get these images ready for VBM analysis in SPM2. While the
> > >> > process of
> > >> > Brain extracting and SUSAN are going smoothly, and nicely
> brain-
> > >> > extracted
> > >> > and de-noised images are being produced, I can't figure
> where the
> > >> > coordinate
> > >> > system is getting modified. Immediately following Brain-
> > Extraction
> > >> > the "mm"
> > >> > values in FSLview on the X, Y, and Z planes are changing
> from the
> > >> > original
> > >> > ~-90mm to +90mm on say the X-axis, to something like 21090mm to
> > >> > 21170mm.
> > >> >
> > >> > I believe this modification of the raw-coordinates may be
> playing
> > >> > into so
> > >> > difficulties making a custom t1-template from these images
> > down the
> > >> > road.
> > >> > I'm also seeing some changes in the header files evident by
> using
> > >> > avwinfo,
> > >> > in terms of the size of each dimension.
> > >> >
> > >> > Any insight you could offer would be wonderful.
> > >> >
> > >> > Thank you
> > >>
> > >> <bet_details>
> >
>
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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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