Hi - as far as I know, we've not started using that field in the
NIFTI header yet - in fact, it's really the job of whatever software
converts the data from DICOM to nifto to fill-in the slice timing/
ordering information, and probably no-one is doing that yet.
Cheers.
On 2 Sep 2007, at 11:20, Dr. Carol Docherty wrote:
> Hi,
>
> We have recently been looking in detail at the NIFTI header format,
> and are currently a little confused over why it does not appear to
> show any slice timing information (all entries relating to slice
> timing in the header appear to be zero). Is this actually the case,
> and is it perhaps why you might not recommend applying slice timing
> correction in FSL?
>
> Thanks in advance,
>
> Carol
>
> ----- Original Message -----
> From: "Steve Smith" <[log in to unmask]>
> To: [log in to unmask]
> Sent: 29 August 2007 04:21:43 o'clock (GMT) Africa/Casablanca
> Subject: Re: [FSL] slice timing correction (coronal slices)
>
> Hi,
>
> As long as the data has not been re-oriented - i.e. that the "Z"
> dimension still corresponds to the original slicings - then the slice
> timing will work fine. Note that we generally don't recommend using
> slice timing correction though.
>
> Cheers.
>
>
> On 29 Aug 2007, at 00:42, Jaymin Upadhyay wrote:
>
>> Hi,
>> I wanted to perform a slice timing correction of fMRI data obtained
>> in the coronal orientation and
>> also in an interleaved manner. I assume that the present slice
>> timing correction method in fsl3.3. or
>> fsl4.0 is optimal for fMRI data obtained axially. Is this
>> correct? What is the best way to perfom the
>> correction of coronal (interleaved) fMRI data.
>> Thanks for your time,
>> Jaymin
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
>
>
> --
> Dr Carol Docherty
> Postdoctoral MRI Scientist
> Department of Neurophysics
> Max-Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A
> 04103 Leipzig
> Germany
>
> Tel: +49 (0)341 99 40 291
> Fax: +49 (0)341 99 40 221
> Email: [log in to unmask]
------------------------------------------------------------------------
---
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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