There is an automasking done in mri_glmfit. For each voxel, it looks through all the inputs. If one of the inputs is 0, then that voxel is masked out. If you have data where this is expected (eg, VBM-like data), then you can add --no-prune. If this is not expected, then look through your data to see what might be wrong. It might be that one of your subjects is all 0s.
doug
On 01/23/2013 02:49 AM, Jürgen Hänggi wrote:
Dear FS experts
I run a longitudinal analysis, and all steps (cross, base, long) were run without errors. I used QA tools in order to look at the results and all recons are fine.
However, when running glmfit with the --osgm option there is no error message, but there is also no results (sig=0, F=0). In the log I realized that the mask is empty (see below).
Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to Cap_Thickness_LH.glmdir/mask.mgh Reshaping mriglm->mask... search space = 0.000000
What are the most plausible reasons for this empty mask? Should I try the pruning option?
Thanks in advance Regards Jürgen
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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