let me know if the problem is the visualization as Bruce suggests. If not, I'll take a look
On 01/30/2017 12:00 PM, Saltzman, David wrote: > > Hopefully I did this correctly: > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w > > > Thanks! > > > 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 Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > *Sent:* Monday, January 30, 2017 11:55:47 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Fw: Issue with creating inflated surface - > poor surface registration? > Can you upload that subject to our filedrop? See below for link > > > On 01/30/2017 11:19 AM, 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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
