Dear Alex,
This is indeed a detailed question and we do not deal with
spectroscopy data
here so cannot help you with that. We also do not have GE scanners.
The only question I can help you with is that it is no longer the case
that
FSLView prefers either radiological or neurological storage. As long
as the
qform and/or sform information in the nifti file is correct then
FSLView is
just as happy either way around.
I hope someone else can help you with your other questions.
All the best,
Mark
On 11 Oct 2010, at 07:21, Alex Ramos wrote:
> Hello,
>
> MR spectroscopy was taken with a depth of 7 slices along the SI axis
> using a GE scanner. The region of interest from which the MRS was
> taken is manipulated by hand using a mouse with GE software. It
> appears that LPS (right-handed) coordinate system or the RAS (right-
> handed) coordinate system cannot be specified when placing the MRS
> region on the scan. Also, the MRS voxel size is different from the
> T1 voxel size obtained during the scan.
>
> After the scan, Dicom images were converted to Nifti format with
> dcm2nii. The Pfile from the scanner prints the center slice number
> in both Z mm (from XYZ) as 66 and S (from RAS) as 48.3. I enter 0 mm
> for both the X and Y axes and 0 for the Scanner Anatomical
> coordinates for both R and A axes. When entering both Scanner
> Anatomical (0,0,48.3) and XYZ (0,0,66) coordinates into FSLview the
> printed center slice number in the Pfile is correct for the Scanner
> Anatomical coordinate and one slice too superior for the XYZ
> coordinate. We assume that this is due to FSLview including 0 as the
> first slice?
>
> We verify the correct location of the center slice by looking at a
> jpg screen shot of the GE monitor when the MRS was done. The center
> slice number on the screen shot corresponds to the Pfile XYZ
> coordinate (0,0,66); however, this number, 66, is given in the Pfile
> as the slice where the MRS was prescribed. No specific coordinates
> are shown in the jpg of the scanner screen shot. We are certain that
> the correlations between the Pfile, the screen shot, and the Nifti
> images we have allow us to select the correct Nifti image to view in
> FSLview.
>
> This screen shot gives a 2D graphic of the center and borders of the
> MRS region of interest in sag, cor, and axial views, so the position
> of the MRS roi is roughly known. The Pfile reports the coordinates
> of the MRS roi in an RAS coordinate system. It seems that the
> scanner interprets the MRS box made with a mouse using an RAS
> system. I assume that transformation matrices are used to generate
> the RAS coordinates for the MRS roi, but I can't seem to find them.
>
> The RX xyz csi volume dimensions from the Pfile appear to correlate
> to the mm volume of the MRS roi, which was made standard across
> subjects, but the reported x volume should be the y volume (and the
> y volume should be the x volume) . When entering the RX xyz csi
> volume center into FSLview, the center is not in the correct
> position (even if we swap the x and y values). I don't know if the
> RX xyz csi values correspond to the center of the MRS roi, the
> center of the MRS's center voxel, or the center voxel of the T1
> scan. I assume it's MRS related because the volume reported
> correlates to the MRS roi.
>
> The Pfile also reports the (R,A,S) Center coord of plane image. When
> these coordinates are entered into the Scanner Anatomical options in
> FSLview, the center is correct but it is one slice too inferior.
> This is confusing because when entering (0,0,48.3) the correct slice
> is viewed along the SI axis (axial plane).
>
> The Pfile gives the coordinates of the top left, top right and
> bottom right handed corners. Do these values correlate to the MRS
> center voxel or the MRS roi or the center voxel of the T1 scan? When
> I enter them into the Scanner Anatomical spaces in FSLview the R, A,
> and S coordinates are off for all considerations. It seems that when
> entering the R and A values into Scanner Anatomical values in
> FSLview they need to be swapped along with a sign change to the R
> value? But this is uncertain. It is something we have just intuited
> at best. I assume that transformation matrices converting the MRS
> roi coordinates to the LPS Dicom format to the RAS Nifti format are
> not printed in the Pfile, Dicom header, or Nifti header.
>
> I have viewed the sform matrix and the offsets using fslhd -x,
> calculated the dicom matrix by using cross products of the two-
> column two-row array with correct sign changes, and the inverses of
> both of these.
>
> The MRS roi cannot be exported after making it with the GE scanner
> software.
>
> Our goal is to reproduce the MRS roi in FSLview so that coordinates
> may be used to extract the exact roi using fslroi. Right now we have
> a rough roi at best using the screen shot. Metabolite data will
> then be generated from a proton density roi of the same and location
> as the MRS roi. The PD roi is flirted to the space where the MRS was
> prescribed. Resampling is done using a variety of fsl tools.
>
> I read on this forum that FSLview has problems reading "radiological
> data" because it "prefers" "neurological data." I don't know which
> of these two formats the data is collected from the GE scanner. I
> also tried using functions like fslorient and fslswapdim to try to
> remedy the problem of using the Pfile RAS coordinates to reconstruct
> the MRS box or the MRS voxel in FSLview.
>
> Could someone please help? I realize that there are numerous issues
> raised here and that each requires a fair amount of depth.
>
> Thank you,
> Alex
>
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