Yes, that does look excessive. There should be a "masks" volume that gets created. This will have the individual masks for each subject. You can load this something like
tksurfer fsaverage lh inflated -overlay masks.mgh -fthresh 0.5 -t masks.mgh
ie, load it as an overlay and timecourse. When you click on a point, the time course will show your the value at each subject, and you can look for subjects where it is 0.
You should also do this with the cesvar map (that's probably where your problem is).
doug
Sid Kundu wrote:
Hi Doug,
Thanks for the help, was able to get the group analysis to work. However, I went back and looked at the mask that was being created and passed into the glmfit and got what's shown in the attached pictures. The ammount of zero valued voxels seems really high. Not sure if this is out of the ordinary or not, but might indicate a problem somewhere else in my analysis. _________________________________ Sid Kundu Biomedical Engineering Boston University
On Thu, Jan 26, 2012 at 11:59 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try the version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concat doug Sid Kundu wrote: Hi Doug, The --prune argument doesn't work with mri_concat in the version of freesurfer I am using. Any other way to accomplish this? _________________________________ Sid Kundu Biomedical Engineering Boston University On Wed, Jan 25, 2012 at 3:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: I'm guessing that there is a voxel (or more) in cesvar that is 0 for a subject (or more). Usually such voxels are masked out by pruning the input ces. You can create your own mask with mri_concat tal.cs.nii tal.cesvar.nii --prune --o junk.mgh mri_binarize --i junk.mgh --min .00000000000001 --o newmask.mgh Then pass this mask to mri_glmfit with the --mask option. doug Finnegan Calabro wrote: Hi Doug et al, We're running into a problem doing a wrfx group analysis using FreeSurfer 4.5. Looks like the glmfit is having trouble with the weights. We tried running it for different subsets of our subjects, and get the same thing, so it's not one subject contaminating the analysis. Any guess where we should look for tracking this down? Presumably the cesvar files are screwed up somehow, which would imply something went wrong in the individual selxavg3's. But any ideas about what could lead to this? The individual overlays all seem to look ok. [sidkundu@brodmann all-vs-null]$ mri_glmfit --y tal.ces.nii --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii --wls tal.cesvar.nii $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null cmdline mri_glmfit --y tal.ces.nii --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii --wls tal.cesvar.nii sysname Linux hostname brodmann.bu.edu <http://brodmann.bu.edu> <http://brodmann.bu.edu> <http://brodmann.bu.edu/> machine x86_64 user sidkundu FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii logyflag 0 usedti 0 mask ../tal.mask.nii maskinv 0 glmdir tal.wrfx.osgm IllCondOK 0 DoFFx 0 wFile tal.cesvar.nii weightinv 1 weightsqrt 1 Creating output directory tal.wrfx.osgm Loading y from /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii Saving design matrix to tal.wrfx.osgm/Xg.dat Matrix condition is 1 Pruning voxels by thr: 0.000000 Found 260736 voxels in mask Saving mask to tal.wrfx.osgm/mask.nii search space = 2.08589e+06 ERROR: MRInormWeights: value less than or eq to 0. c=34, r=2, s=33, v=0 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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Douglas N Greve