Dear Dr. Ashburner,
I tried downloading Deformations-020411.tar.gz from
ftp://ftp.fil.ion.ucl.ac.uk/spm/toolbox/Deformations (as linked from
http://www.fil.ion.ucl.ac.uk/spm/ext/#Def) and installed it in my spm2
toolbox subdirectory. After building the libs, I tried selecting
Toolboxes: Deformations: Deformations from sn3d.mat; changed the filter
in the file selection dialog from *_sn3d.mat to *sn.mat; selected my
.mat; selected default BB; and selected 111 voxdims. Then, the
following error echoed to the matlab console and the GUI hung:
??? Error while evaluating uimenu Callback.
After searching the archives, I tried downloading
ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/spm_sn2def.m; mv
spm_sn3d2def.m spm_sn3d2def.m.orig ; and then ln -s spm_sn2def.m
spm_sn3d2def.m. Although this version didn't let me change from the
default vodims to 111, it did quickly write a y_*img and y_*hdr. But
when I tried to invert this deformation field, the GUI wanted three
files. Since it isn't clear to me how to edit spm_invdef_ui.m to
reflect the new spm2 way of doing things, I wanted to first make sure I
got the right version of the Deformations toolbox.
One other detail, I'm running an ancient version of matlab (5.3.0.10183)
on an SGI Octane IRIX64 1 175 MHZ IP30 Processor.
Thanks much,
Donna
John Ashburner wrote:
>>I spatially normalized an anatomical volume using spm2. I have a
>>surface tesselations of the original anatomical hemispheres; I'd like to
>>apply the spatial normalization (both affine and nonlinear
>>transformations) to these surfaces. Another programmer in our lab used
>>get_orig_coord to do this with spm99 spatially normalized volumes, but
>>said the code was incompatible with the spm2 .mat format. Is there a
>>version of get_orig_coord that works with spm2 generated *sn.mat files?
>
>
> There's no get_orig_coord.m for SPM2 that I know about. I would suggest
> trying the Deformations toolbox, which will allow you to write out a
> deformation field, and invert it. You can then read values from the
> iy_*.img file, to give co-ordinates in spatially normalised space.
>
> Best regards,
> -John
>
|