We adjusted the offset and that was clearly the problem. Looks like it worked great. Thank you so much for clearing this up!
David Saltzman Lab Manager Language and Brain Laboratory Department of Speech, Language, & Hearing Sciences University of Connecticut ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Monday, January 30, 2017 12:01:15 PM To: Freesurfer support list Cc: Rothermich, Kathrin Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration? 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 > > > >
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