Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

freesurfer trouble shooting, anyone help?
by David Soscia 27 Jun '05

27 Jun '05

I am just getting acquianted with the program, and I am running into some difficulties. I have a CD filled with MRI scans in AFNI format (.img, .mat, .BRIK, etc.) and I managed after some time to convert one of my .BRIK files to the .cor extention for Freesurfer. Now I am having trouble opening it. When I go to "open subjects" and try to get to where the file is, is lists a "T1" folder where the folder I have the file in should be, and it will not open. Where can I find this file to open it?...it is still on the CD (that is the location I gave when I converted the file), and also I copied all of the files to another folder on the computer, but when I tried to convert the file from that folder, it did not work. The files that I copied over all now have a pen with a cross through it next to the icon (read only maybe that means?)...I'm not sure because I'm very new with Linux. If anyone can help me, let me know. Thanks, Dave

2 1

re: [Freesurfer] Newbie and some question
by Ngo Trung Thanh 27 Jun '05

27 Jun '05

Thanks a lot. Those really help. However, I don't have the root permission to install those libraries into the required directory. So, I guess that I should use the static version of tkmedit and tksurfer. Could you show me where I can find them? Thanks again. Best, Thanh --- "Bell, Andrew (NIH/NIMH)" <bellah(a)mail.nih.gov> wrote: > Thanh Ngo, > > Welcome to FreeSurfer :) I'm no expert but maybe I > can help. > > I had the same problem (many people have) with the > libtk8.3.so and > libtcl8.3so libraries (I assume you're getting a > "shared library" error). > > Before you try to get the static version to work, > try this: > > Have you searched your computer for these files? > FreeSurfer seems to want > them to be in the /usr/lib directory. If you have > these files but they are > in a different directory, create a symbolic link to > them: > > e.g., if the files are in /opt/tcltk/lib > > cd /usr/lib > ln -s /opt/tcltk/lib/libtk8.3.so libtk8.3.so > ln -s /opt/tcltk/lib/libtcl8.3.so libtcl8.3.so > > > If you don't have these files, you should download > them (make sure you get > version 8.3.x!). If you look on the FreeSurfer > Download page, there is a > link below the table with the main downloads that > takes you to the most > up-to-date binaries. I believe these files are > posted there. > > If you have newer versions of tcl/tk (e.g., 8.4 or > 8.5), you need to install > the older versions as well (make sure to FORCE the > install) -- at least this > was the only way I could get it to work. > > > Hope this helps! > > Andy > > > > Andrew H. Bell, PhD > Laboratory of Brain and Cognition > National Institute of Mental Health > Bethesda, Maryland USA > O: (301) 496-5625 x260 > bellah(a)mail.nih.gov > > > ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

3 2

mris_make_average_surface
by Fornito, Alexander 26 Jun '05

26 Jun '05

Hi, I'm having a little trouble interpreting the mris_make_average_surface usage and was hpoing for some help: usage: mris_make_average_surface [options] <hemi> <output surf name> <canon surface> <output subject name> <subject> ... <output subject name > this program will generate an average of the orig surfaces of all the subjects specified (unless the -s <surface name> flag is used) the transform defaults to talairach.xfm in the subject's mri/transforms directory, but can be changed using the -x <xform name> switch What does the canon surface refer to? Why is there an ouput subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] vertex correspondance they are in correspondence, but there may be shear in the pial deformation, so the link will overestimate the thickness. Easy to compute though, just the distance between the same vertex on the 2 surfaces On Wed, 22 Jun 2005, Fornito, Alexander wrote: > Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 6/22/2005 9:20 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] vertex correspondance > > > > Hi Alex, > > yes, all the surfaces of a hemisphere (except qsphere) have the same # of > vertices/edges and faces. I think Doug has something that will sample the > mask. mri_vol2label or something like that? > > Bruce > > > On Wed, 22 Jun 2005, Fornito, Alexander wrote: > > > Hi again, > > > > So many questions!! > > > > Is there some sort of correspondence between vertices on the inner (wm) > > and outer (pial) surfaces? Ie., for every vertex on the inner surface, > > is there a point on the outer surface, and if so, does Freesurfer retain > > this information in any of the files? > > > > > > > > Also, I have some binary masks that I have manually traced using another > > program that I would like to apply to the surfaces to get regional > > measures of thickness. The mask images are in analyze format. Is there > > any way that I can do this? > > > > Thanks as always, > > > > Alex > > > > > > > > > > > > Alexander Fornito > > > > M.psych (Clin. Neuro.)/PhD candidate > > > > Melbourne Neuropsychiatry Centre and Department of Psychology > > > > The University of Melbourne > > > > alexander.fornito(a)wh.org.au > > > > > > > > > > >

2 1

Newbie and some questions
by Ngo Trung Thanh 25 Jun '05

25 Jun '05

Hi, I installed FreeSurfer in Linux and ran some test on my data. The Volume Processing step and Create Surface step ran smoothly. >From the guide, after these steps, I can view the result by clicking on the Volume button and Surface button. But these, two buttons do not work. I tried to run the tkmedit command but it generate an error of loading libtk8.3.so library. I learned that I can use the static version of tkmedit, but it generated the same error. Also, I found that tksurfer.static is missing in the distribution. Could anyone show me how I can fix this problem and where I can find tksurfer.static? Another question is that after the Volume Processing step, there should be some skull stripped data. Is there any ways that I can convert these data into some familiar 3-D image formats, like MINC or Analyze, so that I can view it in another program. Thanks a lot. Best, Thanh Ngo __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

defining labels
by Kirk, Gregory 23 Jun '05

23 Jun '05

Hello, I remember a message from Bruce to use mris_anotomical_stats -l label to generate statistics for a region, but unfortunatly I cannot find how to define a label, docs do not seem to tell, a quick start tip please. G.

2 2

question on documentation
by Glenn Lawyer 22 Jun '05

22 Jun '05

Hi, We just saw a discussion between Alexander, Doug, Bruce, and Nick about mris_glm which mentioned the FSGDF file. I had not heard of using a group descripter file before, as the statistical aspects of Freesurfer are not covered in (my copy of) the manual or tutorial (downloaded from surfer....harvard.edu/docs/ in the last week). I will start using one, as it provides a more elegant approach than a desing matrix. Not knowing how to write a GDF, I did a google search and found this link: http://surfer.nmr.mgh.harvard.edu/docs/fsgdf.txt, which was very informative. This page, however, appears to be an orphan; I could not find a link to it from any page starting from surfer....harvard.edu/. What other documentation is "hidden" in the docs/ section of your web page? I have found all of the freesurfer documentation to be very helpful, but I have not found all of the documentation. +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

2 1

Questions regarding monkey reconstructions
by Andrew H Bell 22 Jun '05

22 Jun '05

Fellow FreeSurfers, I have a few (more) questions regarding high-res monkey reconstructions. Forgive my naivete - I'm still quite new to this program: I've managed to strip the skull and surrounding muscle tissue (mri_watershed -r 60 -h 15 -wat <in> <out> did the trick) I am now trying to segment, fill and create surfaces. Questions: 1) What is the relationship between mri_segment and control points? I've added a whole whack of control points but they seem to have no effect on the segmentation. How do I influence the segmentation because I'm missing several areas of white matter. 2) For some reason, when I try to run mri_fill, I get a segmentation fault. I'm using the following command: mri_fill -PV 124 138 116 -CV 124 106 116 wm filled I've also tried to enter the above values for the cutting planes in the EXPERT PREFERENCES (as per the manual) and use the interface to fill the white matter, create surfaces, etc. It runs to completion and splits the two hemispheres ok but lops off the top portion of the left hemisphere. 3) Getting back to control points, I've placed a bunch of control points in white matter that seems to get missed. However, when I look at the result after adding these points, they are hanging in empty space (i.e., they don't seem to have any effect). I'm sure this won't be the last of my questions. I appreciate all the help so far!! Thanks!!!! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0921 mobile: (202) 679-1279 bellah(a)mail.nih.gov

2 1

RE: [Freesurfer] vertex correspondance
by Fornito, Alexander 22 Jun '05

22 Jun '05

Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance Hi Alex, yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that? Bruce On Wed, 22 Jun 2005, Fornito, Alexander wrote: > Hi again, > > So many questions!! > > Is there some sort of correspondence between vertices on the inner (wm) > and outer (pial) surfaces? Ie., for every vertex on the inner surface, > is there a point on the outer surface, and if so, does Freesurfer retain > this information in any of the files? > > > > Also, I have some binary masks that I have manually traced using another > program that I would like to apply to the surfaces to get regional > measures of thickness. The mask images are in analyze format. Is there > any way that I can do this? > > Thanks as always, > > Alex > > > > > > Alexander Fornito > > M.psych (Clin. Neuro.)/PhD candidate > > Melbourne Neuropsychiatry Centre and Department of Psychology > > The University of Melbourne > > alexander.fornito(a)wh.org.au > > > >

2 1

vertex correspondance
by Fornito, Alexander 22 Jun '05

22 Jun '05

Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files? Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this? Thanks as always, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

2 1

some data for FreeSurfer presentation
by Renat Yakupov 21 Jun '05

21 Jun '05

Hello. I was wondering if you could help me with the following. I need to prepare a short ~30 min presentation on FreeSurfer to medium-to-advanced level MRI (e.g. research coordinators and people actually acquiring, processing and analyzing MR data). Are there any resources, in addition to FreeSurfer homepage, on FreeSurfer techniques, data processing, etc? I also need to mention any other software packages that can calculate and analyze cortical thickness and maybe do sub-cortical grey matter segmentation. Is there any other software available for free out there? Any input would be appreciated! Thank you. Regards, Renat.

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