Actually, before tranlating by minus the SPM originator less one, you'd
need to translate +Xmin,+Ymin,+Zmin.
But I doubt that it is necessary to do this at all.
On 07/29/2004 11:37 AM, Donna Hanlon wrote:
Hi Sophie,
Some things to check:
1. The anatomical to which the EPI scans were aligned is in the same
voxdims and orientation as the uncropped anatomical (*.LR.*mnc) used
to generate the SureFit surface.
2. The fiducial surface you're using is the one generated by SureFit,
with no transforms applied.
3. You loaded the appropriate *cropped* params file, which tells the
mapper the Xmin, Ymin, and Zmin values by which the surface must be
translated, along with any padding parameters, if this was not a full
hemisphere.
What I confess is not clear to me is if the map_fmri_to_surface
program will try to center the volume based on the SPM originator
voxel in the .hdr, when mapping to an individual surface. John
Harwell would know. In that case, then the vtk surface would need to
be translated -- probably by this amount:
-78,-112,-50 (default bounding box)
-90,-126,-72 (template bounding box)
This assumes cubic 1mm voxels, as required by SureFit.
Donna
On 07/29/2004 11:30 AM, Sophie Riches wrote:
Hello again! Sorry to keep bothering you but i keep getting foiled!
I have aligned a set of EPI fMRI scans to a structural T1 scan in SPM
99 before processing the fMRI data.
The output from SPM looks okay - the activation is where I expected
so I think the orientation is ok and in normal SPM orientation. When
overlaid on slices it appears to be nicely aligned.
However when I map the fMRI to the reconsrtucted surface (from
SureFit) it is quite clearly not aligned at all. I am using the
map_frmi program on windows and have put in the fidiucial file as the
mapping surface,
Have I missed out a step? I have used the parameter file for the
surface and it has set the origin automatically .(although I thought
the origin of a surface made in SureFit would be 0,0,0 so I tried
that and still get it misaligned.) It certainly looks as though it is
in the right orientation but is not centred on the same origin.
Any ideas?
Sophei
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