Dear Douglas, This fails just on this one. Image seems good. I attached it in the previous mail but being held. Thanks!
Best Regards, Yi -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, November 16, 2017 11:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull] does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it? On 11/16/2017 11:32 AM, Yi Li wrote: > Hi FS expert, > > When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform > failed. Please see the attached log file. Is there a way to correct the > error? Thanks! > > Best Regards, > Yi > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Monday, November 13, 2017 5:48 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [strip skull for unregistered images] > > Hi Yi > > yes, brainmask.mgz is the skull stripped image. > > And no, n3 is pretty gentle so I would think letting our normal intensity > normalization run would be fine (and better than not doing it) > > cheers > Bruce > > > On Mon, 13 Nov 2017, Yi Li > wrote: > >> Hi Bruce, >> >> Thanks for the help! Is the skull-stripped image in Brainmask.mgz? >> >> Another question: since my raw image has gone through B1 correction >> and >> N3 normalization, will you suggest I omit the nu and normalize step in >> -autorecon1? >> >> Best Regards, >> Yi >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Monday, November 13, 2017 10:50 AM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] [strip skull for unregistered images] >> >> Hi Yi >> >> autorecon1 should do the skull stripping, so there is no need for the >> separate mri_mask call. The threshold of '5' is so to preserve edits >> in which voxels are turned 'off' (they are set to 1 I believe, but we >> reserve >> 2-4 as additional 'off' values). >> >> The masking will not transform the voxel coordinates of the image >> >> cheers >> Bruce >> >> >> On Mon, 13 Nov 2017, Yi Li wrote: >> >>> Dear FS experts, >>> >>> >>> >>> I would like to strip skulls from unregistered images which have gone >>> through GradWarp, B1-correction, N3 normalization and phantom-based scaling. >>> I run the following two commands in freeSurfer: >>> >>> recon-all -autorecon1 -subjid <subjid> >>> >>> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz >>> >>> >>> >>> My questions are >>> >>> 1) Currently I use 5 as threshold (-T 5). Is there a guidance >>> for the setting of this parameter? >>> >>> 2) In the output file T1.final.mgz, is the skull-stripped image >>> represented in ijk space (image index space) or in XYZ space (via >>> transformation matrix)? >>> >>> 3) If the skull-stripped image is represented in XYZ space, how >>> do I get it in ijk space? >>> >>> >>> >>> Thanks in advance for the help! >>> >>> >>> >>> Best Regards, >>> >>> Yi Li (PhD) >>> >>> Senior Computational Scientist >>> >>> Computational Sciences >>> >>> The Jackson Laboratory >>> >>> Farmington, CT 06032 >>> >>> Tel: 860-837-2156 >>> >>> >>> >>> --- >>> >>> The information in this email, including attachments, may be >>> confidential and is intended solely for the addressee(s). If you >>> believe you received this email by mistake, please notify the sender >>> by return email as soon as possible. >>> >> --- >> >> The information in this email, including attachments, may be confidential >> and is intended solely for the addressee(s). If you believe you received >> this email by mistake, please notify the sender by return email as soon as >> possible. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > --- > > The information in this email, including attachments, may be confidential and > is intended solely for the addressee(s). If you believe you received this > email by mistake, please notify the sender by return email as soon as > possible. > > > _______________________________________________ > 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 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 . 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