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 <[email protected]> wrote: > >> I have total of 46 subjects with pre and post scans....44 subjects were OK >> using the stable version. >> >> Catherine >> >> >> From: Bruce Fischl <[email protected]> >> To: Rongxiang Tang <[email protected]> >> Cc: Nick Schmansky <[email protected]>; Zeke Kaufman >> <[email protected]> >> 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 <[email protected]> >> > To: Rongxiang Tang <[email protected]> >> > Cc: Nick Schmansky <[email protected]>; Zeke Kaufman >> > <[email protected]> >> > 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 <[email protected]> >> > > To: Rongxiang Tang <[email protected]> >> > > Cc: Bruce Fischl <[email protected]>; Zeke Kaufman >> > > <[email protected]> >> > > 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 <[email protected]> >> > > > To: Rongxiang Tang <[email protected]> >> > > > Cc: Nick Schmansky <[email protected]>; Zeke Kaufman >> > > > <[email protected]> >> > > > 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 <[email protected]> >> > > >> To: Rongxiang Tang <[email protected]> >> > > >> Cc: "[email protected]" <[email protected]> >> > > >> 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 <[email protected]> >> > > >> > To: Rongxiang Tang <[email protected]> >> > > >> > 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 <[email protected]> >> > > >> > > To: Rongxiang Tang <[email protected]> >> > > >> > > Cc: "[email protected]" >> > > >> <[email protected]> >> > > >> > > 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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