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.
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