I am currently trying to work with the Haxby (2001) dataset in SPM (data can be downloaded at http://data.pymvpa.org/datasets/haxby2001/).
According to the associated papers, each volume represents 40 64x64 saggitally-acquired slices.
Displaying one of these volumes in SPM, we have:
Dimensions: 40 x 64 x 64
Vox size=-3.5 x 3.75 x 3.75
Dir Cos:
1 0 0
0 1 0
0 0 1
Origin: 20.5 32.5 32.5
The problem I am having is that spm_slice_timing wants a 64-element vector for the slice order, presumably to correct for slice acquisition time along the z-axis, which is inappropriate for these data (Haxby et al. never reported doing slice time correction, so this may have previously been a non-issue).
Is there an elegant solution to the problem? The only thing that comes to mind is the heavy-handed use of some NifTi data manipulation tool to rotate the volumes 90 degrees about the y-axis. Indeed, this may not even solve the problem if whatever tool I use updates the NII headers, and SPM adjusts by reading off along a different axis.
Thanks
|