On 1/15/19 1:26 PM, Dowling, Kevin Francis wrote:
>
> Hello FreeSurfer Experts,
>
>
> I'm writing to follow-up on my question about incomplete lhrh cortical
> and mni305 subcortical masks in preproc-sess. My initial email is
> copied below, but briefly when running WLS functional analyses via
> mri_glmfit in FS 5.3, I noticed a number of large regions that were
> pruned out?in my subcortical and cortical analyses. I traced these
> pruning problems back to subjects' whose raw and fmcpr.siemens.nii.gz
> data are fine for all functional runs, but for whom some pre-processed
> runs had brain.mni305.nii.gz, brain.fsaverage.rh.nii.gz, and
> brain.fsaverage.lh.nii.gz masks that were missing voxels/vertices (0
> values rather than 1s) that cause the pruning problem later on in
> mri_glmfit.I tried pre-processing a number of these problematic
> subjects in FS 6 and noticed that these missing voxels/vertices were
> all fixed. However, as our analysis has ~200 subjects and is
> multi-modal in nature, I would like to avoid re-doing all of our
> analyses in FS 6.0 unless absolutely necessary.
>
>
> Since the fmcpr.siemens.nii.gz functional data looks fine to me for
> the problematic subject runs (as do the brain.nii.gz and
> brain.e3.nii.gz masks), I thought something might possibly be amiss
> with the registration in the mni305 mask generation command (below).
> Specifically,when I look at the output of this command for the
> problematic runs relative to the good runs, the mask
> brain.mni305.2mm.nii.gz looks like it has been rotated away from the
> normal orientation (see attached image, rotated_mask_questionable.png).
>
>
> mri_vol2vol --mov
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/masks/brain.nii.gz
> --reg
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/022/register.dof6.dat
> --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/022/masks/brain.mni305.2mm.nii.gz
>
>
> When I look at the analogous surface command (below), there are
> similar problems, that result in a mask missing 50% of its vertices:
>
>
> mri_vol2surf --mov
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/masks/brain.nii.gz
> --reg
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/022/register.dof6.dat
> --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA161_Testing/bold/022/masks/brain.fsaverage.rh.nii.gz
> --noreshape --cortex --surfreg sphere.reg
>
>
> Looking at the structural functional alignment for this subject with
> tkregister-sess -s GDDA161_Testing -per-run -fsd bold, the
> registration (from register.dof6.dat) seems fine (mincost .57 for this
> problem run, but looks good visually).?Since the use of the
> register.dof6.dat file is common to these two processes, and since FS
> 6.0 uses register.dof6.lta rather than the .dat file, my? inclination
> was to suspect there was a registration issue except that, again,
> visualizing register.dof6.dat via tkregister-sess is fine.
>
>
> Forgive this somewhat naive question, but beyond checking the input
> (which seems fine) and output (which is bad) of this command along
> with the subject's structural/functional registration, is there
> anything else I could do to further troubleshoot this issue? Is there
> a different registration file I should be looking at, or alternatively
> am I looking too far downstream in the preproc-sess pipeline? I would
> be most grateful for any additional troubleshooting ideas.
>
>
> I have attached a .txt file containing the debug output for the
> described subject, whom is an extreme example of the pruning/masking
> issue. The problem run is 022.
>
>
> Thank you again for any thoughts or suggestions you might have!
>
>
> 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
>
>
> ------------------------------------------------------------------------
> *From:* Dowling, Kevin Francis
> *Sent:* Tuesday, January 8, 2019 2:40 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* preproc-sess mask issue
>
> 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