Jolinda,
Just a comment on the statement about DICOM images: What is numbered your
1st DICOM slice depends on your scanner settings - it can be anything from
Head->Feet, Feet->Head, interleaved... So this is a tricky question as
well.
Volkmar
On Fri, 28 Apr 2006, jolinda wrote:
> Hi,
>
> I have one last, relatively minor, question. Make that two questions. FEAT
> uses the native slicings. However, if a file is converted directly from
> DICOM to NIfTI, the native slicings might be expected to correspond to the
> raw data order in the DICOM file, which (ignoring R/L for now) is inverted
> top-to-bottom compared to the Analyze order. Another way to state this is
> that most DICOM viewers plot the data starting at the upper-left corner of
> the view, and most Analyze viewers start plotting from the bottom. So, in
> the FEAT report, axial slices will be nose-down, sagittal slices will be
> head-down, etc. I was just wondering if there were any plans to include a
> flag to switch this, or to use the qform/sform data to detect which way to
> plot the data.
>
> I've modified my conversion program to produce an FSL-specific NIfTI output,
> as well as a regular NIfTI output. The FSL-specific version differs in the
> following ways:
>
> 1. Unsigned 16-bit data is flagged as the signed-16-bit data type, rather
> than the unsupported unsigned-16-bit data type. This is acceptable for most
> (all that I've seen, anyway) MR data, as it uses only the first 12 bits.
>
> 2. The data is flipped along the row axis (LR for axial data) and rotated
> 180 degrees in the image plane. This is equivalent to a top-bottom flip, if
> you prefer to think of it that way. The net result is image data stored in a
> left-handed system, LAS for axial images. This will eliminate any need for
> FSL to invert the data later, and will give a "normal" view in the FEAT
> report. The qform fields should indicate the relationship between the data
> ordering and the NIfTI RAS space.
>
> Is there anything else I should be aware of regarding FSL's use of the NIfTI
> format?
>
> Jolinda
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Mark Jenkinson
> Sent: Saturday, April 22, 2006 2:02 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Yet another orientation question
>
>
> Hi,
>
> As Steve said, we try to display in the native slicings in FEAT. We will,
> however, swap the x-axis in both FSLView and slices (used by FEAT to
> generate the report) if the data is "neurologically" stored. So this means
> that you'll see a "radiological" view of the data,
> although
> the current version should helpfully put right-hand markers (small "R"s) in
> the images to make it clear where the right-hand side is. This will be
> correctly interpreted from the qform or sform information regardless of
> whether it is "radiologically" or "neurologically" stored.
>
>
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg
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