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.
- 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