[Insight-users] problem reconstructing an MRI image in ITK

[robert behan]

Hi Don,

Many thanks for your swift reply. I will have to double check but I
think the data I am trying to reconstruct was acquired using a simple
spin echo sequence ( or a fast gradient echo sequence ) with an 8
channel brain coil. I am trying to get ITK to produce an image for one
slice and one coil and then I will subsequently develop the code to do
a sum of square reconstruction.

It is confusing because I can populate an ITK image using the k-space
data and produce an image using the absolute values of the k-space
data. I write the image to a Dicom file and export it into Matlab. I
can compare the image against an image of k-space produced from the
same GE P-file data but using a Matlab MRI Recon script instead.

I then produce an ITK image with the same complex k-space data but
defined as a complex image type and apply the fft vnl
complex-conjugate to real filter on it and the result is just
garbage!!

I think you may be right it appears to be a problem with how I have
ordered the data.

There is also a line of baseline values in the k-space data which may
be causing a problem.

I have a script in Matlab which can reconstruct MRI images from raw GE
Pfiles and I have noticed a number of things. If the baseline isn't
removed before the ifft is applied then the result is garbage
(basically just an image of gray lines of varying intensity). The same
applied if you try to apply the ifft to the absolute value of the
complex k-space data rather than the complex data itself or if the
complex k-space data is reshaped into a matrix of the wrong size.

I am not exactly sure what the problem is but I do think it is
something along these lines. Any additional insights or suggestions
are more than welcome,

Cheers,

Rob

On 15 November 2010 17:31, Don Bigler <dcb210 at psu.edu> wrote:
> Hi Rob,
>        Reconstructing on MRI image from k-space can be very tricky depending on the pulse sequence used and the method by which the vender stores k-space data to disk.  What pulse sequence did you use to acquire the data?  It sounds to me like you need to reorder the k-space data before performing the FFT.  Did you view the k-space data first before reconstruction?  That can help point you in the right direction.
> Regards,
> Don
>
> Don Bigler, Ph.D.
> Postdoctoral Scholar
> Center for Emerging Neurotechnology and Imaging
> Penn State University College of Medicine
> 500 University Dr.
> Psychiatry, C5518
> Hershey, PA 17033
> Phone: (717) 531-7963
> Fax: (717) 531-6491
>
> Hershey Confidentiality Statement:
>
> This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law.  Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty.  If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately.
>
>