 |
 |
Hi, Cameron.
I haven't tried this yet in SPM5, but with SPM2, I found that I could preserve spatial information simply by reslicing with ImCalc. In other words, I would select the image from ImCalc, then specify that the new image would be resliced withouth any mathematical manipulation (simply 'i1'). The resliced image would have spatial information stored with it, and I could use this image for aligning other images (either through coregistration or through realignment).
Hope this helps.
Doug Burman
==============Original message text===============
On Wed, 09 Jul 2008 5:06:29 pm CDT Cameron Craddock wrote:
Hello all,
I have some fMRI data that was reconstructed offline and all of the spatial
location information is lost in the process. Previously I have been able to
copy this information from another scan that is acquired during the same
session with the same slice prescription using the following scr
ipt.
M0=spm_get_space(file_with_good_center);
spm_get_space(file_with_bad_center,M0);
I am using nifti files.
I have recently upgraded my Matlab version and installed the latest SPM
patches and now this procedure no longer works in two ways:
1). The location mat is only changed for the first volume in the 4D nifti
files. This is easily corrected using a loop.
2). The image orientation after this procedure is not correct. Attached is
a screen capture from spm. I copied the mat information from the top image
to the bottom image. I have verified that the mat information in the
headers are the same by using spm_vol. I have also verified the header
information using AFNI's 3dinfo. AFNI also shows the images in the same
manner as SPM.
Is there some other header information that I need to modify to get this to
work correctly? Is there another method that I could use that
might work?
Thanks in advance for any and all comments.
Here is my system information:
RHEL 5.0 running on quadcore intel Xeon 64bit
Matlab 2008a
SPM5 with Updates_1782
I have recompiled SPM and haven't had any other problems.
Regards,
Cameron Craddock
===========End of original message text===========