Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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

RE: [Freesurfer] mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Fantastic. I really appreciate all your help!! -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 11:00 PM To: Fornito, Alexander Cc: Freesurfer Mailing List; Bruce Fischl Subject: RE: [Freesurfer] mris_glm Alex, Attached is the make_average_surface script. Copy it to the freesurfer/bin directory, and be sure to make it executable (run 'chmod 755 make_average_surface' in the freesurfer/bin directory). Type 'make_average_surface' to get help. Basically, just the subject names are required. By default, a 'subject' named 'average' will be created from your set of subjects (a name instead of 'average' can be specified on the command line). Nick ps. I am working on the mris_surface seg-fault problem using the rh.orig file that you sent. On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > Hi Alex, > > you're better off using the make_average_surfaces.csh script to make an > average of your subjects. Nick: can you send Alex a copy? > > thanks, > Bruce > On Tue, 21 Jun > 2005, Fornito, Alexander wrote: > > > Def. sounds worth doing then! I'll give it a try. > > My other question is, where can I get my hands on the average7? It's > > used as the target in the mris_glm examples, but I haven't been able to > > find the actual average7 surface in any of the freesurfer directories. > > Am I missing something? > > Thanks again, > > Alex > > > > -----Original Message----- > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: Tuesday, June 21, 2005 4:11 PM > > To: Fornito, Alexander > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] mris_glm > > > > > > You can run with just the design matrix, but you won't be able to use > > the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to > > specify how to build the des mtx. The fsgdf keeps track of what the > > regressors mean (eg, Age, Class, IQ, etc). When you save the > > preprocessed data with --y, you'll see that there will be an fsgdf > > file saved with it. Load this in tksurfer, click on a point, and you > > will be able to make a scatter plot of, say, thickness vs age, with > > each class (eg, Male, Female) having a different color dot in the > > scatter plot. When you mouse-over the dot, it tells you the subject > > name. Click on a new point and you'll see the scatter plot for that > > point. If you use --xmat, you can save the design matrix (in matlab-4 > > format). > > > > doug > > > > > > On Tue, 21 Jun 2005, Fornito, Alexander wrote: > > > >> Hi, > >> > >> I was seeking some clarification re: the relationship between the > > fsgdf > >> and design matrix file for use with mris_glm. It seems to me that the > >> two contain very similar info, the examples in the -help don't use the > >> fsdf at all. Is it necessary to create one, or can you just run an > >> analysis with the desmtx? > >> > >> Thanks, > >> > >> 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 > >> > >> > >> > >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

RE: [Freesurfer] mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to specify how to build the des mtx. The fsgdf keeps track of what the regressors mean (eg, Age, Class, IQ, etc). When you save the preprocessed data with --y, you'll see that there will be an fsgdf file saved with it. Load this in tksurfer, click on a point, and you will be able to make a scatter plot of, say, thickness vs age, with each class (eg, Male, Female) having a different color dot in the scatter plot. When you mouse-over the dot, it tells you the subject name. Click on a new point and you'll see the scatter plot for that point. If you use --xmat, you can save the design matrix (in matlab-4 format). doug On Tue, 21 Jun 2005, Fornito, Alexander wrote: > Hi, > > I was seeking some clarification re: the relationship between the fsgdf > and design matrix file for use with mris_glm. It seems to me that the > two contain very similar info, the examples in the -help don't use the > fsdf at all. Is it necessary to create one, or can you just run an > analysis with the desmtx? > > Thanks, > > 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 > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

3 2

mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Hi, I was seeking some clarification re: the relationship between the fsgdf and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the -help don't use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx? Thanks, 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

ERROR: nu_correct
by Margaret Duff 17 Jun '05

17 Jun '05

Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 ######################################## program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ####################################### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev --------------------------------------------- MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -------------------------------------------------------------- mri_motion_correct2 logfile is ./mri_motion_correct2.log -------------------------------------------------------------- ----------------------------------------- Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... ----------------------------------------- Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... ----------------------------------------- Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write ----------------------------------------- Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:................................................................................................................................................................................................................................................................Done ----------------------------------------- Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:................................................................................................................................................................................................................................................................Done ----------------------------------------- Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16:18:41 EDT 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Fri Jun 17 16:18:41 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on troy:/local_mount/space/troy/1 201855952 169100440 32755512 84% /autofs/space/troy_001 ------------------------------------------ recon-all exited with errors at Fri Jun 17 16:18:53 EDT 2005

2 2

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