Hi Jeff,
If you are still having the machine-specific problems with Analyze
format
then it is probably safer to convert these images to nifti format using
avwchfiletype. This should work straightforwardly, but check it in
fslview just to make sure.
All the best,
Mark
On 1 Jun 2006, at 20:06, Steve Smith wrote:
> 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>
>> >
>>
>
>
> -----------------------------------------------------------------------
> ----
> 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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