Hi David

I'm not sure that there is anything actually wrong, I think what you are
seeing is just a visualization issue. The inflated surfaces
will overlap when viewed together in freeview, since they are
centered on each hemi and inflated. You can use the :offset=x,y,z modifier
for the -f ?h.inflated to move them left/right so they don't overlap if you
want.

cheers
Bruce


On Mon, 30 Jan 2017, Saltzman, David wrote:

>
> Hello FreeSurfer Developers,
>
>
> We have attempted to run the standard recon-all pipeline on multiple MRI
> datasets, and seem to be encountering the same error. While the recon-all
> log does not indicate there are any errors (so far as we can tell as
> novices), when we look at the inflated surfaces, there is clearly some
> problem creating the inflated surface, in that the hemispheres appeared to
> be mirrored. For the purpose of simplicity, we will include the log and scan
> information for the most recent anatomical scan we have to run the recon-all
> pipeline on. I believe the attached screenshot (anterior coronal view) will
> make the issue more apparent.
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
> Mac OS 10.12
> 3) recon-all.log: see attached
> 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
> -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner)
> 5) Scan information: 
> Data Axes Tilt:  Oblique (15.784 deg. from plumb)
> Data Axes Approximate Orientation:
>   first  (x) = Anterior-to-Posterior
>   second (y) = Superior-to-Inferior
>   third  (z) = Right-to-Left   [-orient ASR]
> R-to-L extent:   -80.718 [R] -to-    94.282 [L] -step-     1.000 mm [176
> voxels]
> A-to-P extent:  -188.767 [A] -to-    58.233 [P] -step-     1.000 mm [248
> voxels]
> I-to-S extent:  -186.650 [I] -to-    68.350 [S] -step-     1.000 mm [256
> voxels]
>
> Any help would be tremendously appreciated!
>
> Thanks,
>
>
> David Saltzman
>
>
> Lab Manager
>
> Language and Brain Laboratory
>
> Department of Speech, Language, & Hearing Sciences
>
> University of Connecticut
>
>
>
>