oh, we had this problem briefly. Maybe the .m3z format changed? Can't
remember. How many subjects do you have?
On Tue, 19 Feb 2013, Rongxiang Tang wrote:
> Hi Bruce,
>
> The error is :
>
> #@# SubCort Seg Tue Feb 19 03:30:54 EST 2013
>
> mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z
> /home/virtualuser/apps/freesurfer/average/RB_all_2008-03-26.gca
> aseg.auto_noCCseg.mgz
>
> MatrixAsciiReadFrom: could not scanf parms
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -renormalize_mean 0.500
> -regularize 0.500
> not handling expanded ventricles...
> reading 1 input volumes...
> reading classifier array from
>
/home/virtualuser/apps/freesurfer/average/RB_all_2008-03-26.gca...
> reading input volume from norm.mgz...
> average std[0] = 6.9
> reading transform from transforms/talairach.m3z...
> zcat transforms/talairach.m3z
> Segmentation fault
> Linux FreeSurfer 2.6.28-19-generic #66-Ubuntu SMP Sat Oct 16 17:39:04 UTC
> 2010 i686 GNU/Linux
>
> recon-all -s 1452 exited with ERRORS at Tue Feb 19 03:31:25 EST 2013
>
> Thanks,
> Catherine
>
>
> ____________________________________________________________________________
> From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> Cc: Nick Schmansky <
nicks@nmr.mgh.harvard.edu>; Zeke Kaufman
> <
zkaufman@nmr.mgh.harvard.edu>
> Sent: Tuesday, February 19, 2013 9:02 AM
> Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
>
> Hi Catherine
>
> you need to tell us what the error is. The command line you specify below
> will run autorecon2 since you told it to. Try -make all instead of the rest
> and see if it works. It's supposed to only recreate what is needed.
>
> cheers
> Bruce
>
> On Tue, 19 Feb 2013, Rongxiang Tang wrote:
>
> > Hi Nick,
> >
> > The new downloads worked, however I ran into some new problems....
> > I only replaced the three binaries and when I
ran autorecon2, there is
> > always error message with mri_rmneck...so I replaced that binary with the
> > dev version and the error disappeared. But then for the subsequent steps I
> > ran into more error.
> > My guess is that I have to replace all binaries with the dev version? My
> > worry is that since there are only four subjects that need the dev version
> > to run, and the rest of the subjects were all proceesed with the stable
> > v.5.0.0...would updating all binaries to the dev version cause
> inconsistency
> > with the results?
> >
> > another question about the command line...since the recon-all was killed
> at
> > mri_rmneck...if I want to rerun the analysis right from where it was
> > stopped, how do i do that?
> > I have tried to use recon-all -rmneck -autorecon2 -autorecon3....but
> somehow
> > it
just ran from the beginning of autorecon2...
> >
> > Thanks,
> > Catherine
> >
> >
> >___________________________________________________________________________
> _
> > From: Nick Schmansky <
nicks@nmr.mgh.harvard.edu>
> > To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> > Cc: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>; Zeke Kaufman
> > <
zkaufman@nmr.mgh.harvard.edu>
> > Sent: Sunday, February 17, 2013 10:26 AM
> > Subject: Re: [Freesurfer] talairach
transformation troubleshooting problem
> >
> > for the virtual box ubuntu, you'll want the centos4 build (not the
> > centos4_x86_64 build, which is 64b).
> >
> > Nick
> >
> >
> > > Hi Bruce,
> > >
> > > Thanks for the advice. I'm running the recon-all with the new files...
> > > About updating the binaries...I'm currently using the VirtualBox Ubuntu
> > > 32b on windows to run the analysis. The version of free surfer I'm using
> > > is v5.0.0. I actually downloaded the
> > > freesurfer-Linux-centos4_x86_64-dev.tar.gz from the website, and update
> > > the 3 binaries you mentioned...however when I ran the recon-all, the
> > > terminal notifies me that these three binaries file are not executable.
> > >
> > > I was wondering if I need to update the entire
binaries?
> > >
> > > Thank you,
> > > Catherine
> > >
> > >
> > >
> > > ________________________________
> > > From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> > > To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> > > Cc: Nick Schmansky <
nicks@nmr.mgh.harvard.edu>; Zeke Kaufman
> > > <
zkaufman@nmr.mgh.harvard.edu>
> > > Sent: Friday, February 15, 2013 5:04 PM
> > > Subject: Re: [Freesurfer] talairach transformation
troubleshooting
> problem
> > >
> > > Hi Catherine
> > >
> > > I'm not entirely sure what went wrong, but running the current dev
> > > versions of mri_em_register/mri_ca_normalize/mri_ca_register fixes the
> > > problem. I'll attach the relevant files. Put the talairach.lta and
> > > talairach.xfm in the mri/transforms dir, and the norm.mgz and
> > > aseg.auto_noCCseg.mgz in the mri dir, and try running recon-all -make
> all
> > > -s <subject name>
> > >
> > > actually the talairach.m3z is too big. Maybe the best thing to do is to
> > > update your binaries and try it with the new ones and see if that fixes
> it
> > > for you. What hardware/software env are you using? Nick or Zeke can get
> > > you the right versions. I'll filedrop the .m3z
> >
>
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu, 14 Feb 2013, Rongxiang Tang wrote:
> > >
> > >> Hi Bruce,
> > >>
> > >> The aseg is also problematic for several slices....I uploaded the
> > >> subject dir on the Matinos center file drop...since the
> > >> file is too big, I separated into two parts.
> > >>
> > >> Thanks,
> > >> Catherine
> > >>
> >>>_________________________________________________________________________
> __
> > ________________________________________________
> > >> From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> > >> To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> > >> Cc: "
freesurfer@nmr.mgh.harvard.edu" <
freesurfer@nmr.mgh.harvard.edu>
> > >> Sent: Thursday, February 14, 2013 2:42 PM
> > >> Subject: Re: [Freesurfer] talairach transformation troubleshooting
> > >> problem
> > >>
> > >> probably not, although it's hard to say. If you upload the whole
> subject
> > >> dir I'll take a look. How does the aseg look?
> > >> On Thu, 14 Feb 2013, Rongxiang Tang wrote:
> > >>
> > >> > Hi Bruce,
> > >> >
> > >> > I
checked the skullstrip stage using this command:
> > >> >
> > >> > tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs....
> > >> > and both of the brainmask and T1 images look fine.... the wm.mgz is
> > >> problema
> > >> > tic, with some area missing..... I was wondering if I need to
> manually
> > >> adding control points to solve the pro
> > >> > blem.
> > >> > Thanks,
> > >> > Catherine
> > >> >
> > >>>__________________________________________________________________________
> _
> > _
> > >> > From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> > >> > To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> > >> > Sent: Thursday, February 14, 2013 2:03 PM
> > >> > Subject: Re: [Freesurfer] talairach transformation troubleshooting
> > >> problem
> > >> >
> > >> > Hi Catherine
> > >> >
> > >> > that looks like something went wrong in the surface recon, not in the
> > >> > talairaching. Maybe a skullstrip problem? You need to investigate.
> > >> Also,
> > >> > please cc the list so that others can answer!
> > >> >
> > >> > thanks
> > >> > Bruce
> > >> > On Thu, 14 Feb 2013, Rongxiang Tang wrote:
> > >> >
> > >> > > Hi Bruce,
> > >> > >
> >
>> > > I attached two images...one is the target view and the other is the
> > >> > moveable
> > >> > > view.
> > >> > >
> > >> > > Thanks,
> > >> > > Catherine
> > >> > >
> > >> > >
> > >>>>_________________________________________________________________________
> _
> > _
> > >> > _
> > >> > > From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> > >> > > To: Rongxiang Tang <
rongxiangtang@yahoo.com>
> > >> > > Cc: "
freesurfer@nmr.mgh.harvard.edu"
> > >> <
freesurfer@nmr.mgh.harvard.edu>
> > >> > > Sent: Thursday, February 14, 2013 1:33 PM
> > >> > > Subject: Re: [Freesurfer] talairach transformation troubleshooting
> > >> problem
> > >> > >
> > >> > > Hi Catherine
> > >> > >
> > >> > > can you send us an image of what you are looking at?
> > >> > >
> > >> > > thanks
> > >> > > Bruce
> > >> > > On Thu, 14 Feb 2013,
> > >> > > Rongxiang Tang wrote:
> > >> > >
> > >> > > > Dear All,
> > >> > >
>
> > >> > > > When I was checking the talairach transformation output, I
> noticed
> > >> that
> > >> > > some of the white matter was not included inside
> > >> > > > the green line. Instead of drawing the green line to include all
> > >> of the
> > >> > > white matter of the whole brain, it somehow only
> > >> > > > includes the bottom half of the white matter of the brain.
> > >> > > >
> > >> > > > Is there a way to fix that?
> > >> > > >
> > >> > > > Thanks,
> > >> > > > Catherine
> > >> > > >
> > >> > > >
> > >> > >
> > >> > >
> > >> > > The information in this
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> > >> > > contains patient information, please contact the Partners
> Compliance
> > >> > > HelpLine at
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http://www.partners.org/complianceline . If the e-mail was sent to
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