Hello FreeSurfer Experts,
I'm writing with a question about a potential problems that has come up in my functional analysis. I'm running FS version 5.3 on a Linux (at the Martinos Center - CentOS release 7.6.1810).
I was recently running osgm WLS analyses with mri_glmfit and the --prune flag when I noticed that a large number of vertices in my surface based analysis were pruned out due to no signal (about 40% of the entire surface, see attached an example image of a group analysis that includes one of the bad subjects: pruning_issue.png). My first thought was that this result was potentially due to a poor functional/structural alignment for some subjects. However, I re-checked my functional and structural alignments, along with the quality of the recons, and they all look good. Upon further inspection, I observed similar erroneous pruning problems affecting voxels in the mni305 space (for an example see pruning_issue2.png). This issue stems from a modest number of subjects that have first level analyses with large amounts of no signal. Indeed, removing these problematic subjects from group surface based analyses resolves most of the excessive surface pruning problems.
When I look at the fmcpr.siemens.nii.gz files for the runs in the problematic subjects' directories the processed functional data looks good, but when I visualize the fmcpr.siemens.sm5.mni305.nii.gz (and ...fsaverage.lh.nii.gz / ...fsaverage.rh.nii.gz) files it is clear that an inappropriate number of voxels (/vertices) have been masked out. When I look at the brain.mni305.nii.gz, brain.fsaverage.rh.nii.gz, and brain.fsaverage.lh.nii.gz masks I can see they are missing a large number of voxels/vertices that should be in the masks, which leads me to think that something may be going wrong in the lh/rh/mni305 masking/mask generation step (though brain.nii.gz and brain.e3.nii.gz masks look fine to me). I've looked through the archives and wasn't able find a similar issue discussed previously.
I was therefore wondering what might be causing this mask issue (given the alignments appear to be good) and what might be the best way to go about correcting this error. Would I need to manually edit all of these masks to include the missing voxels/vertices if the automatic generation failed or is there a better solution someone might be able to suggest?
My preprocessing command is: preproc-sess -s SubjectID01 -surface fsaverage lhrh -mni305 -d $SUBJECTS_DIR -fsd bold -stc siemens -fwhm 5 -per-run
I would be happy to send along mask files/other files should they be of help.
Thank you in advance for any suggestions you might be able to provide!
Best wishes, Kevin
Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215 He / Him / His
