Dear Kate,
I can't answer the question about the sform setting. But you can check
image alignment within SPM with CheckReg - just select all images you want
to display simultaneously.
Hope this helps,
Volkmar
On Mon, 29 Aug 2005 [log in to unmask] wrote:
> Hi,
>
> I used SPM5b, revision 218, DICOM import function to convert
> 2 Siemens DICOM volumes to nifti. One volume was an MPRAGE, 1 slice
> per dcm file, the other was a functional image in DICOM mosaic format.
>
> Why did the conversion set the sform ? I thought there would only
> be a qform setting indicating the "scanner-anatomical" coordinates.
> Is there an additional "put it in SPM default space" translation, or did
> it convert to a Talairach space, and in any case wouldn't the sform code
> be something besides 1 ?
>
> The DICOM MPRAGE was sagittal, and the functional was axial. I would
> now like to see whether I can use the nifti coordinate info to get
> a good overlay/alignment of the functional on the structural.
> Is there an SPM5b command or nifti_tool way to get a transformation
> to reslice an image, based on its qform/sform info, and another image's
> qform/sform info, to align image one into image two's space ? Since
> the two images were collected during the same scan session, I am
> assuming that the world coordinates are the same across both volumes.
> I would like to get an image resliced on disk, eg in a nifti file,
> not just in memory.
> I appended the relevant nifti header info (via nifti_tool) below.
>
> thanks
> Kate
>
> -----------------------------------------------------------------------
> header file 'f050411120628-0007-00088-000088-00.hdr', num_fields = 43
> pixdim 76 8 -1.0 3.125 3.125 3.0 0.0 0.0 0.0 0.0
> descrip 148 80 2.89362T 2D SE\EP
> TR=2000ms/TE=25ms/FA=70deg 11-Apr-2005 13:3:4.2225 Mosaic
> qform_code 252 1 1
> sform_code 254 1 1
> quatern_b 256 1 0.0
> quatern_c 260 1 0.983255
> quatern_d 264 1 0.182236
> qoffset_x 268 1 100.0
> qoffset_y 272 1 -91.569847
> qoffset_z 276 1 -79.26651
> srow_x 280 4 -3.125 0.0 0.0 100.0
> srow_y 296 4 0.0 2.917439 -1.075104 -91.569847
> srow_z 312 4 0.0 1.1199 2.800741 -79.26651
>
>
> header file 's050411120628-0019-00001-000192-00.hdr', num_fields = 43
> pixdim 76 8 -1.0 0.78125 0.78125 1.0 0.0 0.0 0.0 0.0
> descrip 148 80 2.89362T 3D IR\GR
> TR=1570ms/TE=3.04ms/FA=8deg 11-Apr-2005 14:3:57.89
> qform_code 252 1 1
> sform_code 254 1 1
> quatern_b 256 1 0.582745
> quatern_c 260 1 -0.40051
> quatern_d 264 1 -0.582745
> qoffset_x 268 1 -95.5
> qoffset_y 272 1 116.978775
> qoffset_z 276 1 -55.748558
> srow_x 280 4 0.0 0.0 1.0 -95.5
> srow_y 296 4 -0.72936 -0.279975 0.0 116.978775
> srow_z 312 4 -0.279975 0.72936 -0.0 -55.748558
>
>
--
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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