Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

directional cosine error?
by Nguyen, Thang Q 01 Jun '06

01 Jun '06

Hello all, I get a directional cosine error when I try to register data or extract values from them so I tried mri_info and get this message: mri_info subj1.img matfile: only read 256 bytes of name (810698068 specified) MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile subj1.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find subj1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in subj1.mat file ----------------------------------------------------------------- Volume information for subj1.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 79.0000 0.0000 2.0000 0.0000 -95.0000 0.0000 0.0000 2.0000 -68.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 -0.0000 -0.0000 39.5000 0.0000 0.5000 0.0000 47.5000 0.0000 0.0000 0.5000 34.0000 0.0000 0.0000 0.0000 1.0000 Here is the mat file: Subj1 2.000000 2.000000 200.000000 1.054861e+00 -2.348376e-02 -1.086195e-01 7.747378e-01 9.350572e-02 -3.302234e-01 1.067427e+00 -3.124532e+01 -4.640190e-02 -9.299399e-01 -3.056859e-01 -7.546637e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round What does the matlab error mean? Why can't it read the directional cosine? -Thang

2 1

error in 'create surface'
by Joongnam Yang 01 Jun '06

01 Jun '06

Hi all, I posted a question, but for some reason, I didn't get any response. Please help me on this. Here is the question. I ran 'process volume' and 'create surface' on csurf. The created surface (left inflated) has brain stem attached to it. So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. No change took place. I tried commandline 'recon-all -stage1 -subjid ID', with no luck. Would someone suggest any comment on this? Nam.

2 1

Problems with Auto Reconall
by Frederick Powell 01 Jun '06

01 Jun '06

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.117 0.005 0.077 -0.516; -0.015 1.062 0.148 -22.126; -0.084 -0.173 1.230 -34.192; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... Segmentation fault Linux killiany 2.6.9-34.ELsmp #1 SMP Wed Mar 8 00:27:03 CST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Wed May 31 16:54:11 EDT 2006 Above are the errors that I have recieved while trying to run the latest version of auto recon. Please help I am continuously getting teh Segmentation Fault error. I am running 3t MPRAGE images. Thanks -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

2 1

Using cortical segmentation in an anatomy project
by Ivan Blagoev Topolsky 01 Jun '06

01 Jun '06

Hello ! I work for the department of Anatomy (http://www.medecine.unige.ch/GRAC/) in the Centre Médical Universitaire of the Université de Genève (http://www.unige.ch/) We're planning to use the FreeSurfer software suite (or more precisely, the surface-based stream ) in a project that aims to synthesize brain models for teaching through rapid-prototyping (like 3D-printing) out of brain MRI, thus by-passing and giving an alternative to using dead human bodies for teaching. I have 2 questions relative to this project : - Does anyone here have recommendations (or references) about MRI sequence parameters to obtain best contrast for optimal segmentation ? Our preliminary test data wasn't top quality indeed, and we're planning to obtain new datasets. Does anyone has some tips to give us ? - The download page mentions that the source code will be soon released (https://surfer.nmr.mgh.harvard.edu/fswiki/Download?action=highlight&value=s…) but that we'll have to wait until all non-releasable modules are replaced with open-source-able ones. How far has the OS'ing effort gone until now ? Most specifically, which modules are already OS'able ? And how much effort remain to be done ? When will we see an OS'ed version ? Under what license are those sources going to be released ? (GPL, BSD, other ?) Thank you and have a nice day. - Ivan Topolsky -

3 2

Cortical thickness difference measurement
by Joao Pereira 01 Jun '06

01 Jun '06

Hello again! Firstly, let me thank you for your precious previous advices, which pointed me in the right direction. I have another question for you: I have read your article on Reliability of MRI cortical thickness measurements and its relation with scanner and field, and I would like to know what function did you use to subtract the subjects' average cortical thickness files in order to have a cortical thickness difference layer. I don't know if this is a very basic question, but I can't seem to find how to do it with FS. Thank you! Joao Pereira

2 1

question about flattening surfaces
by adam walczak 31 May '06

31 May '06

Hello, I was searching through the wiki and ran across a page that said to use csurf to make full surface cuts in order to ultimately create flattened surfaces. But while perusing the support archives, it was said that csurf is no longer supported. Is this true? How then do you make the full surface cuts needed to create the flattened surfaces? Thanks Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 9

mghWrite failure in mri_remove_neck
by Graham Wideman 30 May '06

30 May '06

Folks: In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that: 1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz 2. But then appeared to perform the neck removal anyway and write the output 3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz ... and sure enough, there is no such file there. The recon-all.log for these steps is copied below. This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory. I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for? But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it). Clues? Thanks, Graham =============== #-------------------------------------- New invocation of recon-all Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ####################################### [...] #@# Remove Neck Mon May 29 03:13:29 PDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006

4 13

brain stem elimination
by Joongnam Yang 30 May '06

30 May '06

Hi all, I ran 'process volume' and 'create surface' and found that brain stem was attached to the left inflated brain. So, I editted 'wm' slices and got rid of the parts related to the brain stem in all slices. and ran 'create surface' again, but no change took place in the 'inflated brain'!!! Would someone suggest a solution to this? p.s. I ran 'recon-all' but it didn't make a difference, either. Nam.

1 0

Reconstruction -> cortical maps without using Talairach transform
by adam walczak 30 May '06

30 May '06

Hello, I want to make cortical surface images that we will overlay with our own masks. But we want to do this in native space. So, I was wondering if it is possible to go thorugh the reconstruction process to make the surfaces without ever using the talairach transform and keeping everything in its native space. Thank you, Adam adam --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.

3 9

problems with group analysis (mri_glmfit?)
by Lars M. Rimol 30 May '06

30 May '06

Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right? Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong? There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial: [lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt--glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731 $Id: mri_glmfit.c,v 1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done ------------ This is my FSGDF: $ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ -- yours, LMR

3 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