Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

Would adjusting watershed parameters change pial surface?
by Jake Freimer 02 Aug '06

02 Aug '06

I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake

2 1

aseg.stats
by Doug Greve 01 Aug '06

01 Aug '06

I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy. The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities). The values in the table (ie, volumes and intensities) should be exactly the same. This change only applies to dev (not to stable) and should be live on Tue. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

5 13

tkmedit problem
by Anthony Steven Dick 01 Aug '06

01 Aug '06

Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 ....and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: -------- freesurfer-Darwin-tiger-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR /Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR /Applications/freesurfer/mni/bin MINC_LIB_DIR /Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB /Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony

2 2

need a list of segmented subcorical regions and their intensity values...
by Shahabuddin Ansari 31 Jul '06

31 Jul '06

Hello, I have seen a list of 40 freesurfer-segmented subcortical objects with their respective intensity values somewhere in the documentation, but not able to locate it now. Could somebody help me please. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Freesurfer August 2006