Freesurfer July 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
88 discussions

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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mgh format wiki doc: Error; additions
by Graham Wideman 13 Jul '06

13 Jul '06

Folks: (Probably Nick S?) Comments on the MghFormat wiki doc page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fMghFormat 1. Width/Height/Depth confusion. -------------------------------- Doc says... width integer first dimension of the image buffer (slowest) height integer second dimension of the image buffer (2nd slowest) depth integer fastest dimension when reading the buffer ... yet mriio mghWrite(...) source code says... for (frame = start_frame ; frame <= end_frame ; frame++) { for (z = 0 ; z < depth ; z++) { for (y = 0 ; y < height ; y++) { [...] for (x = 0 ; x < width ; x++) Ie: width should be fastest, and depth slowest, contrary to doc. Further, the statement "the bytes being read in the order Z --> Y --> X" is either incorrect or doesn't have any meaning. 2. "image data starts at specified offset, which is currently ???". -------------------------------------------------------------------- Looks like from the source code that the header is padded to 24 + 256, which means image starting at byte 280 (counting from zero). 3. Other Data -------------- In the doc, the Other Data section ends at "FoV". Actually the source code shows that mghWrite writes out other stuff beyond that, which in the examples I looked at appears to be a history of commands performed on the image so far, for example (abbreviated [...] and wrapped by me): =========================== [...] mri_convert /data/[...]/39174a/mri/rawavg.mgz [output filepath] --conform ProgramVersion: $Name: stable3 $ TimeStamp: 06/06/07-04:10:32-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlin[...] CompilerName: GCC Compile[...] mri_ca_normalize -mask brainmask.mgz nu.mgz [...] norm.mgz ProgramVersion: $Name: stable3 $ TimeStamp: 06/06/11-05:41:45-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlin[...] GCC CompilerVersion: [...] =========================== (Plus the source code suggests that if a Talairach transform has been applied it appears here in some form). ----------------------------- Graham

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mri_label2label validation failed
by Darren Weber 13 Jul '06

13 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Doug et al., I'm trying to test mri_label2label because we've observed some strange results in the download for: freesurfer-Linux-rh9-stable-pub-v3.0.2 To test the program, I thought it would be sensible to map a label of one subject onto itself, with a different label filename for the output. So I created a large label in a subject rh inflated surface and saved it to X.label file. I then tried to run mri_label2label using the same srcsubject and target subject, with a different name for the target label, ie: mri_label2label \ - --srclabel $SUBJECTS_DIR/${srcsubject}/label/$label \ - --trglabel $SUBJECTS_DIR/${srcsubject}/label/$newlabel \ - --srcsubject ${srcsubject} \ - --trgsubject ${srcsubject} \ - --regmethod surface --hemi $hemi --trgsurf pial In effect, this should be equivalent to: cd $SUBJECTS_DIR/${srcsubject}/label/ cp $label $newlabel That is, the label mapping onto the same subject surface should be identical. It is not. Can you please try to replicate this result? I would like to know if it is particular to the setup here. If you find a bug in mri_label2label, please forward a fix ASAP, as we are trying to complete some analysis that depends on mapping labels across subjects. Thanks, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEtDeZxaCYN7qs0v4RApcvAKCBTkFl5dOPIaAVD0Qv5vejQ7E+3wCglb2U LXK6ke2GQGjDITqafbLtVGk= =5OcG -----END PGP SIGNATURE-----

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cortical thickness table.
by Chacko Cherian 13 Jul '06

13 Jul '06

Hello all, The cortical thickness table which is located in the stats folder..i am currently opening it with my vi editor.Is there any way to open it directly as a spreadsheet to print it out?? THanks Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Freesurfer July 2006