Dear Daryl,
> In coregistering/reslicing data from TMS/fMRI studies, SPM is cutting areas
> of interest under the TMS coil because lower signal there. How can I force
> SPM to use my mask (changing the Default option to Optional Mask didn't
> seem to help) or set my own thresholds for for voxel inclusion?
We've had the exact same problem using spiral sequence at Stanford - to
get around it, I wrote a small program that many people there use
routinely now. The program helps:
1) create an anatomically defined mask (from the subject's anatomy),
2) apply this mask explicitly to the individual analysis model (by
changing an SPMcfg.mat file), and
3) estimate the individual level results using this anatomical mask.
The program and a description of how to use it can be found on:
http://www-psych.stanford.edu/~kalina/SPM99/Tools/glm_specmask.html
This issue has been discussed previously on the SPM mailing list - if you
are interested in more details, see:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0112&L=spm&P=R2965&I=-3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0012&L=spm&P=R8685&I=-3
Best,
Kalina
_________________________________________
Kalina Christoff, Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge, CB2 2EF, U.K.
Tel: +44 (0) 1223 355294 Ext 723
Fax: +44 (0) 1223 359062
Email: [log in to unmask]
_________________________________________
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