Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

"Failed to find brainstem" in monkey volume
by peggy christidis 13 Oct '05

13 Oct '05

I'm helping out an intern here who is working on monkey volumes in FreeSurfer. He has gotten to the point where he has a decent looking white matter segmentation, but when he tries to proceed with filling the white matter, he says he gets the following error: "Failed to find brain stem". At this point I don't have any additional information to give you (sorry), but has anyone ever encountered this problem? Any idea what "failed to find brain stem" might mean? Thanks, peggy

3 2

labeling question
by Erin.Slason＠UCHSC.edu 12 Oct '05

12 Oct '05

We are using the development version of freesurfer in our lab for segmenting brains. In the parcellation process, the superior temporal gyrus is labeled as a whole, but specific parts of the STG including the planum temporale (which we need) are not being labeled. The labeling process used is curvature.buckner40.filled.desikan_killany. If we use a different labeling process, such as atlas2005, will these structures be labeled? If not, is there another way to approach this problem? Thanks. Erin Slason Professional Research Assistant Neuromagnetic Imaging Center Department of Psychiatry University of Colorado Health Sciences Center 303-315-5459 Erin.Slason(a)uchsc.edu

2 1

hardware recommendations?
by L.Scheef＠uni-bonn.de 11 Oct '05

11 Oct '05

Dear list members! I wonder if anybody could recommend me hardware for a dedicated freesurfer PC. Any suggestion? Also, should I stick to Redhat 9 or is it worth to go for the new SUSE/Redhat distributions? Many thanks for your help and best wishes, Lukas _______________________________________________ Dr. Lukas Scheef, Dipl. Phys. FE: MRT/fMRI Dep. of Radiology University of Bonn 53105 Bonn Germany

4 4

invalid command name "PNG"
by xmeadow＠uchicago.edu 10 Oct '05

10 Oct '05

Hi, I've got a Mac box running OS X 10.3.9 and Freesurfer ,v 1.3 2003/08/05 19: 19:16, and just recently when I start up freesurfer I get an error. To reproduce the error I do: >source /Applications/Freesurfer/SetUpFreeSurfer.csh Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $ FREESURFER_HOME /Applications/Freesurfer FSFAST_HOME /Applications/Freesurfer/fsfast AFNI_DIR /Applications/Freesurfer/afni FSL_DIR /Applications/Freesurfer/fsl SUBJECTS_DIR /Users/xmeadow/subjects >csurf & Application initialization failed: invalid command name "PNG" Then Freesurfer opens up normally. I was just wondering what this error message means. I've looked online and seen that PNG stands for 'Portable Network Graphics' (I think), but I don't know if I have it installed or if I need it installed. Is there something I can do to get Freesurfer to load without errors? Thanks very much. >Xander

3 5

aseg visualization
by Bruce Fischl 10 Oct '05

10 Oct '05

Hi All, if you are generating aseg volumes DON'T overlay them on the T1 volume. It is only for cortical processing, as the intensity normalization that creates it will erode the borders of the thalamus and the pallidum. Overlay the segmentation on the norm (or orig) volume in order to assess it's accuracy. cheers, Bruce

1 0

Subcortical questions
by Fornito, Alexander 09 Oct '05

09 Oct '05

Hi, Just wandering if there are any options for improving the results of the subcortical segmentation. It seems to label to large an area for many structures (eg., white matter gets included in the thalamus label). Also, are the surfaces through the midline of the subcortex (ie., the portion labelled as 'medial wall' bu the parcellation step) used during ther spherical registration for the cortex? I'm wandering if I need to pay attention to how the surfaces look in these areas or not. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

2 1

subcortseg with files processed with older version
by walhovd＠nmr.mgh.harvard.edu 07 Oct '05

07 Oct '05

Hi We've some data processed with the FS version prior to the dev version. Now we want to subcortically label these, but when recon-all -subcortseg -segstats -subjid <subject name> we get error:cannot find nu/COR-info understandably, since there is no nu for the old version. Is it possible to work around this so that it doesn't use that? It all works excellently if we do the preprocessing (autorecon1) again with the new version, but if possible it would be great to avoid that because the brain volumes of many of these have been edited for stuff like vessels and skullfragments. Thanks, - Kristine

2 1

difference between dev version and the final stable version?
by Renat Yakupov 07 Oct '05

07 Oct '05

Hi FreeSurfer community, I have a question about the current dev release - how different is the new 'stable' release going to be different from it? Is it mostly stability and compatibility between different platforms issue? Or are the actual processing or computational steps going to be different also? Can I start processing some brains using dev release and then continue processing using new 'stable' release? Or process half of my images with dev release and the other half with new 'stable' release and then do some inter-group comparisons? And another small question - should I also use Red Hat 9 download for Linux Fedora Core 3? Thank you. Regards, Renat.

2 1

PhD-Position; Medical Physics
by Uwe Pietrzyk 07 Oct '05

07 Oct '05

Dear Colleagues, please find attached to this eMail a Word-Document (german/english) describing a PhD-Project in the field of Medical Phyics / Polarized Light Imaging with the topic in brain research / connectivity. Feel free to forward this eMail to potentially interested colleagues. Many thanks, Uwe Pietrzyk /---------------------------------------------------------------------- Prof. Dr. Uwe Pietrzyk Diplom-Physiker Institut für Medizin Forschungszentrum Jülich GmbH 52425 Jülich Tel: +49-2461-61 4763 Fax: +49-2461-61 2820 + 8229 Mobil: +49-172-213-2155 eMail: U.Pietrzyk(a)fz-juelich.de http://www.fz-juelich.de/ime/ime_mitarbeiter_pietrzyk & Bergische Universität Wuppertal Fachbereich C - Physik / D.08.01 Gaußstr. 20 42097 Wuppertal Tel: +49-(0)202-439-3523 Fax: +49-(0)202-439-2811 eMail: Uwe.Pietrzyk(a)physik.uni-wuppertal.de http://www.physik.uni-wuppertal.de ----------------------------------------------------------------------/

1 0

Re: [Freesurfer] Error:
by Michele Grubb 06 Oct '05

06 Oct '05

Thank you Nick! Michele >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 10/5/2005 12:12:44 PM >>> Michele, >From looking at the recon-all.log, it appears that you have an older version of freesurfer than contained a bug whereby mris_anatomical_stat was missing the -mgz flag. You could either: 1) manually run mris_anatomical_stats as shown: cd /home/amc/AMCSubjects/18014B mris_anatomical_stats -mgz -f scripts/rh.aparc.stats -b -a \ label/rh.aparc.annot 18014B rh or 2) install a new 'dev' release of freesurfer and rerun your subject: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Nick On Wed, 2005-10-05 at 11:33 -0400, Michele Grubb wrote: > Ok-here is the file. > > Michele > > >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 10/4/2005 1:49:48 PM >>> > Hi Michele, > > you need to send us more info than this. Preferably the whole > recon-all.log file. > > Bruce > On Tue, 4 Oct 2005, Michele Grubb wrote: > > > Dear FS Help: > > > > When running recon-all -subjid 18014B -autorecon3 -mgz > > > > we got the following error message: > > > > autorecon3 exited with errors- > > ERROR: mris_anatomical_status exited with nonzero status > > > > What does this error mean? What can we do to reconcile this? > > > > Thank you. > > > > Michele > > > > > --------------------------------------------------------------------------------------------------- > > Michele C. Grubb, PhD > > Research Development > > Neurosciences Advanced Imaging Research Center > > 47 New Scotland Ave., MC65 > > Albany, NY 12208 > > > > office: (518) 262-0810 > > fax: (518) 262-0802 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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