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) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > ---------------------------------------------------------------------------- > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
