Yea, the 5.3 stream used FSL brain masking to make the masks for the
fmri. Version 6 uses the FS brain mask transferred into fmri space.
Inevitably, you will have to do a lot of reprocessing. The simplest
thing to do is to delete the mask files in session/bold/masks and
sessoin/bold/RRR/masks (where RRR is the run number). When you re-run
preproc-sess, it will figure out what needs to be re-run. It should not
rerun motion correction, slice timing correction, or registration
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
