Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Hemispheric devision problem
by Akram Bakkour 17 Jul '06

17 Jul '06

Hi all, I've been having trouble with these two brains with huge ventricles, first the aseg failed, and the ventricles didn't get filled automatically, so I filled them manually and ran recon-all -autorecon2-wm but my surfaces were off and there was a blatant hemispheric devision problem with the surfaces, so I added a corpus callosum seed point using recon-all -autorecon2-wm -cc-crs <X Y Z> but that didn't work. I ran out of fixes to try, any suggestions!? Thanks! On machine blakey source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/banzai/3/users/efenster/CLINDEM_processing/ which mri_convert /usr/local/freesurfer/stable/bin//mri_convert cd $SUBJECTS_DIR recon-all -autorecon2-wm -cc-crs 126 98 97 -subjid 06142006_4TTclindem03 subjid 06142006_4TTclindem03 recon-all -autorecon2-wm -cc-crs 129 113 128 -subjid 06212006_4TTclindem04 subjid 06212006_4TTclindem04 check output: foreach s (06142006_4TTclindem03 06212006_4TTclindem04) tkmedit 06142006_4TTclindem03 lh.white -aux wm.mgz -aux-surface rh.white end Notice the hemispheric devision problem with the surfaces. Any suggestions as to how to fix this!? Thanks! Akram.

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Question concerning orientation
by Jake Freimer 17 Jul '06

17 Jul '06

I have run several instances of autorecon2 and have only got left hemisphere data. The log file says that autorecon finished with errors but I can not find where to find these errors. I believe that the problem is the way the data being fed in is oriented so I was wondering how I should reorient it to get it to work. Thanks Jake

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general question concerning orientation
by Chacko Cherian 17 Jul '06

17 Jul '06

Hello everyone, orientation i guess is quite an issue. Well how does,Freesurfer determine orientation of the image.Do I have to know how the image has been processed before it reaches me or is there any other way to find out?Does it have to do with the 'flip'? I checked the orientation of an image on SPM and on Freesurfer. Left on SPM is Right on Freesurfer and vice versa is what I got. Essentially how do I determine L-R orientation? Thanks in advance, Chacko Cherian. Arizona State University. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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recon-all error
by Anil Roy 17 Jul '06

17 Jul '06

Hello All, I've been running recon-all on a couple of minc brains on Fedora Core 4 and everything thing runs fine. I started running a few on a Mandrake Linux 9.2system but each time recon-all exits with errors and I'm unable to see why. I've attached the recon-all.log file and would appreciate any input on why this is occurirng. Thanks, Anil Roy.

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problems running FreeSurfer on a Scyld BeoWulf cluster
by Renat Yakupov 17 Jul '06

17 Jul '06

Hello everybody, Does anybody run FreeSurfer on Linux clusters in general or Scyld BeoWulf clusters in particular? Do you have any problems? We are having some problems running FreeSurfer on our cluster. Quite often when we run autorecon2 stage on a compute node, it crashes. Sometimes a node crashes very quickly, sometimes after hours of processing. All of the 4 compute nodes that we have here have crashed. And it is not hardware related, because I ran linpack on them for 50+ hours in a row, and it was fine. Any ideas what might be causing it? Any suggestions? We run freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz <http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-centos4_x86_64- stable-pub-v3.0.3-full.tar.gz> version, and here is `uname -a` output: Linux scyld.localdomain 2.4.21-37.EL.301r0072smp #1 SMP Wed Mar 1 04:09:49 EST 2006 x86_64 x86_64 x86_64 GNU/Linux Thank you. Regards, Renat.

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OpenGL
by Joe Berens 17 Jul '06

17 Jul '06

Hello, A user gets the following: GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by display: <hostname>:60.0 This is using tightvnc via ssh from a windows xp box to Redhat Enterprise 3. Every thing else seems to work fine. Any Ideas? -Joe A __________________________________________________________________________ Joe Berens Department of Electrical and Computer Engineering University of Minnesota - Twin Cities Phone: 612-625-4585 200 Union Street SE, Room 4-174 Email: joe(a)umn.edu Minneapolis, MN 55455 Office: EE/CSsci 1-183 Department of Psychology University of Minnesota - Twin Cities Phone: 612-625-0644 75 East River Road Email: joe(a)umn.edu Minneapolis, MN 55455 Office: N219 Elliot Hall __________________________________________________________________________

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Misclassified dura
by Dziobek, Isabel 17 Jul '06

17 Jul '06

Hi Everybody, I have a question in regard to the skull stripping and subsequent grey and white matter segmentation. The skull stripping process is faulty with almost all my subjects, leaving large parts of the dura and sagittal sinus. I tried changing the watershed parameters but that did not work (it seems that once parts of the dura are removed, other parts of the more inferior aspects of the brain are removed too). It would be good to have the option to e.g. only eat up some pixels from the top, is that possible? Also, on what is the subsequent segmentation in gray and white matter dependent? It seems that in some cases, although dura and sagittal sinus are still thee after the skull strip, they are correctly not segmented into gray (or white) matter. So I am wondering if the skull strip does not have to be perfect but instead ohter subsequent steps are more important. Is it possible to influence these steps? I am attaching a snapshot of a slide, in which the dura is misclassified as gray matter and the sagittal sinus is not classified at all. Thanks in advance for your help!! Best, Isabel PS. Are there any example scans (other than bert) where I can see how a very good (or good enough) skull strip and segmentation look like?

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autorecon1
by Chacko Cherian 15 Jul '06

15 Jul '06

Hello everyone, I was running recon-all -autorecon1 -s bert and it exited with errors.. Processing... Not implemented yet in cache _volume _range _has _ changed()... IS there anything wrong in the way i've run the command?? THanks in advance for your help. Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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unknown volume
by dasoscia＠buffalo.edu 14 Jul '06

14 Jul '06

When you to the parcellations in autorecon3, you get an unknown volume in middle of the brain. What exactly is in this unknown volume, and why does it label it as such? thanks, dave

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Starting with brain-extracted volume?
by Graham Wideman 13 Jul '06

13 Jul '06

Nick, Doug or anyone with thoughts on the matter, This is a return to a similar question I raised in June-2nd thread "Some FS input questions", but a little less awkward. We'd like to present to FS already brain-extracted volumes that are already "conformed", ie: 256^3, and 1 mm isotropic This would appear to avoid the necessity to turn off aseg (mentioned by Nick in previous thread). I also see the enticing looking options like "noskullstrip", but... I'm wary of two things: a) In general, when you select a "nosomething" option, does recon-all do the right thing to "pass the data through" (usually a copy I suspect) so that subsequent steps receive their input file(s)? b) There may be steps that expect the skull or neck to be in place? "EM Registration with Skull" (skull-lta) sounds like it might be one? So I'd like to know if there are such, and whether I should care? According to my chart here: grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm ...looks like I *should* be able to bypass rmneck and skull-lta (or just let them run unsatisfactorily) with no downstream impact. Any thoughts? Thanks, Graham

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