Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

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

4 11

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.

2 1

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 --

2 1

[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. _____________________________________________________________________________________________

1 0

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.

2 1

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

2 1

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

3 3

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

08 Mar '06

Of course I put the subject name that I prefer to keep hidden! thanks Valentina -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, March 08, 2006 4:03 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: martinos-tech(a)yahoogroups.com; Freesurfer Mailing List Subject: Re: autorecon1 Hi Valentina, did you actually put "<subject name>" on your command-line? <subject name> is supposed to be the name of your subject, eg, "bert" (but without the quotes). What's a "Flug"? For your second question, there will not be a brain.mgz after the first step, but there will be a brainmask.mgz. Also, please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to pose questions so that we can answer them better. thanks doug Durastanti, Valentina (NIH/NINDS) [F] wrote: >Hi, >I have 2 questions: > >Number 1 > when I try to run the first step: > recon-all -subjid <su -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 > > > > > -- 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

1 0

FS-FAST registration across sessions
by Jane Aspell 08 Mar '06

08 Mar '06

Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ------------------------------------------- [Freesurfer] FS-FAST Registration Question: registration across sessions within subjects Tommi Raij Thu, 20 Oct 2005 15:43:46 -0700 Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc- sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to- structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

3 4

Question re' surface simulations.
by zvalim＠gmail.com 06 Mar '06

06 Mar '06

Dear FreeSurfer mailing list, I have looked at the online documentation for the new version, and was wondering where one could find more details on the permutation algorithm implemented in the current version. Some issues I would like to understand better is how the smoothing in the dataset is captured in the algorithm, and what is being permutated at the group level. If there is any reference to a published paper implementing this exact algorithm it would be very useful as well. Specifically, what I found online was: The first parameter the nulltype, which is the method of generating the null data to be tested. Useable options are: (1) perm - perumation, randomly permute rows of X (cf FSL randomise) (2) mc-full - replace input with white gaussian noise (3) mc-z - do not actually do analysis, just assume the output is z-distributed (cf ANFI AlphaSim) I have two questions of this... In (1 perm), what does "X" stand for -- a conditionXsubject table for each voxel? In (2 mc-full), when WN gaussian is inputted, is it smoothed with the characteristics of the original dataset? Sincerely, Uri

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer