Freesurfer March 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
84 discussions

fix vertex area
by Sasha Wolosin 13 Mar '06

13 Mar '06

Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Recon All
by Frederick Powell 13 Mar '06

13 Mar '06

Hello all, I am new to Freesurfer and would like to know what is the new command to perform the automated process for this software. I have created a subject directory and my files are dicom. If anyone could please give me as much information because I just started to use this and I am running X11 on my mac. Any help would be much appreciated. Thanks -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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mgh to something else
by Pellegrini, Stefano (NIH/NINDS) [F] 10 Mar '06

10 Mar '06

Hi everybody, I know that the mgh/mgz format is quite new and there is not much documentation around, yet. I was wondering if there is some procedure already implemented to convert this format to something else, let's say minc format. thanks a lot, -stefano

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Announcement: new stable release, v3.0
by Nick Schmansky 10 Mar '06

10 Mar '06

Freesurfer community, A new stable release, v3.0, is now available. The Release Notes page describing what's new, and a link to the download page, is here: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes All users, including those using prior 'dev' releases, are encouraged to upgrade to this release. Updates to the stable release will be issued if major bugs are found (and fixed), and as new features which do not affect existing functionality become available. The Freesurfer development team

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talairach subject
by Sasha Wolosin 10 Mar '06

10 Mar '06

Dear all, I noticed that there is no talairach subject included in the new release subject's directory. Is the talairach subject no longer needed? Or must it be downloaded separately? Thanks! Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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stable3 vs. stable-pub
by Vasanth Pappu 10 Mar '06

10 Mar '06

Hi, in /usr/local/freesurfer/, there is stable3 and stable3-pub. What is the difference between these two; our group is interested in freezing a copy but not sure which one to pick. Thanks, Vasanth Pappu --

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[Freesurfer] [martinos-tech] New average subject and stable release, v3.0 (fwd)
by Jenni Pacheco 10 Mar '06

10 Mar '06

I am re-sending an email that Doug wrote earlier this week, as it was a thorough description of some pretty important changes to the average subject and talairach subject. There is a new average subject to replace average7 that ALSO replaces the talairach subject. It is called "fsaverage" and can be found in the distribution itself (no additional downloads needed): $FREESURFER_HOME/subjects/fsaverage as an additional note, fsaverage can only be used with subjects processed the new way (i.e., with automatic filling of the entire ventricle). Another average subject that will be compatible with subjects processed the old way (i.e., manual editting of the wm) will be available soon. Please read Dougs email below if you missed it!! Jenni ---------- Forwarded message ---------- Date: Mon, 06 Mar 2006 18:12:55 -0500 From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Reply-To: martinos-tech(a)yahoogroups.com To: martinos-tech(a)yahoogroups.com, Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Subject: [martinos-tech] New average subject and stable release, v3.0 Sorry in advance for the long email ... We have a new average subject that we are recommending that people use instead of "average7". This subject can also replace the "talairach" subject as well. The name of the "fsaverage", and it can be found in the distribution itself: $FREESURFER_HOME/subjects/fsaverage To set up a link in your SUBJECTS_DIR, do the following: cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage There is a README file in $FREESURFER_HOME/subjects/fsaverage that describes how this subject was created. IMPORTANT: Differences between average7 and fsaverage, and FIX_VERTEX_AREA with impacts on mri_surfcluster and mri_glmfit. As some people have noted, the total surface area of average7 was much less than that of a typical subject (by about 40%). This caused the areas of clusters as reported by mri_surfcluster to be too small. HOWEVER, a bug in the routine that computed the vertex area caused the clusters to be 50% too large. So, the net effect was that the clusters were about the right size :). Stay with me. The surface area of the new average subject (fsaverage) is that of a typical subject, SO, it is IMPORTANT that it be used in conjunction with the fixed vertex area. This affects only two programs: mri_surfcluster and mri_glmfit. After today (March 6, 2006), if you use average7 with mri_surfcluster or mri_glmfit, they will give the following error: ERROR: you have selected subject average7. It is recommended that you use the fsaverage subject in $FREESURFER_HOME/subjects. If you really want to use average7, re-run this program with --really-use-average7 as the first argument. If you chose to do so, then it will print out: INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release. The results should be the same as when you ran it prior to the stable3 release. If you have used average7 along with Monte Carlo or Permutation simulation, inferences based on those simulations should still be correct. The only problem will be that the cluster area might be a little different. If you have used a non-average subject as your common surface space or an average subject that you created prior to March 1, 2006, then the cluster sizes will appear to drop by a third the next time your run mri_glmfit or mri_surfcluster. Again, any mri_glmfit simulation results will still be valid. For backwards compatibility, you can add --no-fix-vertex area to either mri_surfcluster or mri_glmfit. The new versions of mri_surfcluster or mri_glmfit will include the following line in their summary/logfile output: # FixVertexAreaFlag 1 The value will either be 1 or 0 depending upon whether it was fixed or not fixed. Again, sorry for the long-winded email. I know this is pretty confusing, so don't hesitate to write with questions as we get this sorted out. PLEASE send questions to the group to help in this process. thanks doug Nick Schmansky wrote: >Freesurfer community, > >A new stable release, v3.0, is now available. >The Release Notes page describing what's new, >and a link to the download page, is here: > >http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > >All users, including those using prior 'dev' >releases, are encouraged to upgrade to this >release. > >Updates to the stable release will be issued >if major bugs are found (and fixed), and as >new features which do not affect existing >functionality become available. > >The Freesurfer development team > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- 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 SPONSORED LINKS Biomedical engineering Biomedical engineering jobs Biomedical imaging _____________________________________________________________________________________________ YAHOO! GROUPS LINKS * Visit your group "martinos-tech" on the web. * To unsubscribe from this group, send an email to: martinos-tech-unsubscribe(a)yahoogroups.com * Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service. _____________________________________________________________________________________________

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dev-version/new version question.
by Martin Ystad 09 Mar '06

09 Mar '06

Hi, I'm currently using the freesurfer-Linux-centos4-dev20060210-full release, and I'm thinking of upgrading to the new stable release. However, I've done a lot of processing with the 20060210-release, and I'm not very keen on starting all over again with the new release. Do you recommend that I reprocess my subjects on the new stable release before doing a group study, or are they similar enough in terms of results, so that I don't need to? In case I do need to run everything over, which steps do I need to rerun (certainly not all?), and can I keep my manual edits to the brainmask- or wm-volume? Thanks, Martin Ystad University of Bergen, Norway.

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Tksurfer problems with the new (Freesurfer 3.0) Mac OS X release
by Anton L. Beer 08 Mar '06

08 Mar '06

Hi, I downloaded the new Mac version of Freesurfer yesterday in the hope that it resolves some tksurfer problems of the old version. However, when I try to start it the following error message comes up: tksurfer CS1b lh inflated dyld: tksurfer Undefined symbols: tksurfer undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib tksurfer undefined reference to _fwrite$UNIX2003 expected to be defined in /usr/lib/libSystem.B.dylib Trace/BPT trap I am using OS X 10.3.9 and I have just updated libSystem, but that didn't solve the problem. The previous version of Tksurfer (October 2005) was running, but it always broke down when trying to make a closed path and then setting another vertex. I would highly appreciate any suggestions about how to fix the new version or how to fix the old tksurfer. Thank you very much. Anton Beer

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autorecon1
by Durastanti, Valentina (NIH/NINDS) [F] 08 Mar '06

08 Mar '06

Hi, I have 2 questions: Number 1 when I try to run the first step: recon-all -subjid <subject name> -autorecon1 He said: ERROR Flug <subject name> unrecognized Number 2 After the first step of a subject I can't find the brain.mgz Thanks Valentina

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Freesurfer March 2006