Hi Catherine Is not ideal. Ou could copy your subjects and try rerunning with dev (keeping edits) Bruce
On Feb 22, 2013, at 12:14 PM, Rongxiang Tang rongxiangtang@yahoo.com wrote:
Hi Bruce,
Just want to follow up on the error issue:
It seems that using the stable version for two of the subjects will always give incomplete surface output....and if using the dev version, it seems to require updating the entire binaries to avoid the error.
I was thinking that if it is ok to use stable version for most of the subjects and use dev version for the two subjects that have problems, and finally run group analysis with the whole data set?
Thanks, Catherine
On Feb 19, 2013, at 10:32 AM, Rongxiang Tang rongxiangtang@yahoo.com wrote:
I have total of 46 subjects with pre and post scans....44 subjects were OK using the stable version.
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 10:27 AM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
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 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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