Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Problems downloading FSfast tutorial data
by McLean John (NHS Greater Glasgow & Clyde) 23 Jul '07

23 Jul '07

Hi, I am trying to download the FSfast tutorial data. So far i have been unsuccessful. I have tried downloading the files from IE and firefox browsers and also via ftp using filezilla, these have all failed. Am i doing something stupid or is it possible there is an issue at the source. Any help greatly appreciated. Best wishes John ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

3 2

Connecting Vertex Points in FreeSurfer
by Troy Mcan 20 Jul '07

20 Jul '07

Hi Everybody,I am bringing in talairach points into freesurfer by converting them into vertexes. I need to connect all of them to create a colored label showing the area bounded by these vertex points. However, I can't seem to find a way to connect these vertexes in a specified manner. I would greatly appreciate any help on the matter.Thanks!Best regards, _________________________________________________________________ PC Magazine’s 2007 editors’ choice for best web mail—award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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statistical designs
by Wang, Xin 20 Jul '07

20 Jul '07

Hello, group I want to learn more about designs of the general linear models for different statistical tests, such as paired T, ANOVA, and correlation tests. Could anybody suggest some examples of the designs for each model? I am facing a few problems of correlation analysis. If I want to do the within group correlation analysis, how can I do it without groups (or classes) as a regressor (if I only have one class and assign a 0 for the group in the contrast, does it work)? How can I specify the pearson's or Spearman's correlation in the analysis? How to know I have enough subjects for this correlation analysis? Thank you in advance, XIn Wang

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Skull Stripping Corrections
by James N. Porter 20 Jul '07

20 Jul '07

Hello- I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meninges. They don't seem too bad: http://www.tc.umn.edu/~norb0062/skull_strip_leftovers.bmp But I'm wondering how much trouble such remnants can cause down the pipeline. That is to say, when performing these checks should I only be concerned with making sure that all skull has been stripped away without taking away any brain, or should I also be concerned with making sure that all non-brain bits have been stripped away? -- Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam

2 1

Create thickness map
by Inês Souta 20 Jul '07

20 Jul '07

Hello, Is it possible to create a "fake" thickness map in order to perform some tests? Thanks, Ines

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How to analysis animal data
by lan lin 20 Jul '07

20 Jul '07

I know someone here have successfully apply freesurfer on monkey. Do you mind to describe how you can do that? Freesurfer is closely related to human atlas. If you need to apply it on animal, like monkey, do you need to contruct a monkey atlas? Anything besides atlas that need to take care? thanks

2 1

Intersecting surfaces (thickness = 0mm)
by Inge K. Amlien 20 Jul '07

20 Jul '07

Hello list, when I process on v3.05 I notice areas where the pial and wm surfaces intersect, giving cortical thickness = 0. This is usually seen in the medial temporal area. Is this a known issue, and how should I deal with it? See attached screenshots. Have a nice day Inge Amlien Department of Psychology University of Oslo ------------------------------ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 RedHat release: Red Hat Enterprise Linux WS release 4 (Nahant Update 5) Kernel info: Linux 2.6.9-42.0.10.ELsmp x86_64 (Hugging Linux)

2 1

mris_volmask
by Ipek Oguz 19 Jul '07

19 Jul '07

Hi, Where can I get the mris_volmask tool? I've seen that it was on the ftp server under pub/dist at some point, but it seems to have disappeared. Thanks a lot! -ipek

2 1

recon-all Is-Running
by Doug Greve 19 Jul '07

19 Jul '07

I've just added a new feature to the dev version of recon-all to help you manage your processes. When you launch recon-all, it will create a file called IsRunning.lh+rh in your subject/scripts folder. When recon-all finishes (with or without errors), this file will be deleted. So, the presence of this file indicates that recon-all is being run on this subject. This file may also exist if recon-all died in a way that it could not clean up (eg, control-C). The contents of the file indicate information about the process that will allow you to determine whether it is still running or not: date Thu Jul 19 19:24:30 EDT 2007 processid 10196 hemi lh rh host icebox user greve Linux icebox 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux You can then ssh to the host and use the unix 'ps' command to check for the existence of the process. If you run recon-all on this subject again while this file exists, it will exit indicating that the subject is already being processed or recon-all died uncleanly. If you want it to run regardless, then add -no-isrunning to the command-line. It will not delete the IsRunning file, just ignore it. When you run the hemispheres separately (ie, -hemi lh or -hemi rh), it will create a IsRunning.lh or IsRunning.rh file. This allows you to run recon-all for both hemis in parallel. If this file exists or IsRunning.lh+rh exists, then again recon-all will exit telling you that the subject is already being processed or recon-all died uncleanly. 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

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gca file format
by lan lin 19 Jul '07

19 Jul '07

I got some question about gca file format. What does totaltraining means? GIBBS_NEIGHBORS is more 6 neighboring voxels. What is relationship between them? From 1:6 , which one is left, right etc? thanks

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