Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

FreeSurfer Newbie can't get working with FSL on Mac OS 10.4
by Marc D. Yelle 29 Jun '06

29 Jun '06

Hello, I am in need of some help. I have spent the last two days trying to get fsl and freesurfer to play well together. I have the newest version of FSL installed and it works perfectly. I then installed freesurfer per the instructions listed in the wiki. After these steps, freesurfer works, but fsl won't open. I get this error message: MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/../System/Library/Perl/5.8.6:/sw/l ib/perl5:/sw/lib/perl5/darwin GSL_DIR /usr/local/freesurfer/lib/gsl TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib MISC_LIB /usr/local/freesurfer/lib/misc/lib FSL_DIR /usr/local/freesurfer/fsl Marc-Yelles-Computer 1% echo $FSLDIR /usr/local/fsl Marc-Yelles-Computer 2% fsl Error in startup script: no suitable image found. Did find: /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) == "wish" } { package require Tk package require Tix tix configure -scheme TixGr..." (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 21 I tinkered with the setupfreesurfer.csh and the freesurferenv.csh files and got it to list FSL_DIR as usr/local/fsl but the program still wouldn't work. If I comment out the two freesurfer lines in my .cshrc file, fsl works perfectly once again. My only guess is that there is a problem with both fsl and freesurfer having tktcl libraries. But my understanding of UNIX, etc is somewhat limited. Below I have also attached my .cshrc : #!/bin/tcsh set path = (/usr/X11R6/bin $path /sw/sbin /sw/bin /Users/marcyelle/bin) set prompt="`hostname -s` \!% " source /sw/bin/init.csh source /usr/local/rsi/idl_5.6/bin/idl_setup setenv IDL_PATH "<IDL_DEFAULT>:+/usr/local/rsi/idl_5.6/local_lib" setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} unsetenv LANG Thank you in advance for your assistance, I need it! Sorry for the long email, I simply wanted to give you as much info as I could. Take care. -- Sláinte, -m Marc D. Yelle Dept. Neurobiology and Anatomy Wake Forest School of Medicine Medical Center Blvd. Winston-Salem, NC 27157 myelle(a)wfubmc.edu

2 1

Anatomical Stats
by Anil Roy 29 Jun '06

29 Jun '06

Hi Everyone, Is there a way to process the minc files I have and only obtain the anatomical stats without the entire recon-all process. I have a large number of brains and it would take a couple of weeks if I was to take every minc file and run recon-all. Thanks - Anil.

2 2

mri_normalize -conform question
by Sebastian Moeller 29 Jun '06

29 Jun '06

Hi List, as the subject line says I am having problems running mri_normalize (on suse 9.3 x86_64, freesurfer centos4 x86_64 3.0.2 release). When feeding in slightly unconformed volumes (like 1mm isotropic 256 by 256 by 256 of type 3 (float)) mri_normalize's "-conform" argument fails (fully unconformed volumes are no problem). The error message boils down to MRInormGentlyFindControlPoints: unsupported src format 3" followed by "MRI3dGentleNormalize failure! mri_ctrl=Null". I just work around this by running a full mri_convert --conform on my input file before running mri_normalize. Just a nit, specifying "-v" some where else than at the end of the commandline easily produces segmentation faults (probably because -v is "overloaded" to also expect Gx Gy Gz arguments? the help is a bit terse) Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

4 11

retinotopy
by Nurunisa Neyzi 28 Jun '06

28 Jun '06

Hi, during retinotopic mapping, still at the beginning, when I run the analysis (with the command sfa-sess), I get the error: ERROR: meanimg for mean image failed meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset -o rtopy/h-offset and I have h.bdhr and omnibus in my eccen and polar folders... and no h volume folder. (I have f.bhdr, fmc.bhdr, fmc.mcdat, my 32 f-stem and fmc-stem data, rtopy.par, inorm.log and mcparams2extreg.log in 001, 002, etc.) what can be going wrong? Thanks! Nurunisa

2 1

Scale Bar
by Reza Rajimehr 28 Jun '06

28 Jun '06

Hi, Does anybody have any idea what the scale bar shows in Tksurfer? I have heard that the scalebar is 10mm for the human brain. I am working with the monkey brain. Is the length of the scale bar 1cm for the monkey brain as well? Thanks, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

2 3

Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Thank you for the response. I may be overly forthcoming here, but when will the next stable release be available. Aju On Thu, 29 Jun 2006 Doug Greve wrote : > >We are still evaluating it, but it should be ready by our next stable release. > >doug > > > >Bruce Fischl wrote: > >>Doug put together a white matter parcellation that does this kind of thing, but I'm not sure what the status of it is. Doug? >>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >> >>>What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. >>> >>>Aju. >>> >>> >>>On Thu, 29 Jun 2006 Bruce Fischl wrote : >>> >>>>what would the white matter volume of a cortical region mean? >>>>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >>>> >>>>>Hello All, >>>>> >>>>>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >>>>> >>>>>Thanks, >>>>> >>>>>Aju. >>>>> >>>>> >>>>>************************************************** >>>>>Mr.Ajith Kumar U >>>>>Junior Research Fellow, >>>>>Department of Audiology, >>>>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>>>Manasagangothri, >>>>>Mysore,570006 >>>>>INDIA. >>>>>Ph: +91 821 2514449 Ext 186 (O) >>>>> +91 821 2514449 Ext 224 (R) >>>>>Fax: +91 821 2510515 >>>>>Email: ajithajitkumar18(a)rediffmail.com >>>>>************************************************** >>>> >>>>_______________________________________________ >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>>************************************************** >>>Mr.Ajith Kumar U >>>Junior Research Fellow, >>>Department of Audiology, >>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>Manasagangothri, >>>Mysore,570006 >>>INDIA. >>>Ph: +91 821 2514449 Ext 186 (O) >>> +91 821 2514449 Ext 224 (R) >>>Fax: +91 821 2510515 >>>Email: ajithajitkumar18(a)rediffmail.com >>>************************************************** >> >>_______________________________________________ >>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 > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. **************************************************

2 1

Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. Aju. On Thu, 29 Jun 2006 Bruce Fischl wrote : >what would the white matter volume of a cortical region mean? >On Wed, 28 Jun 2006, Ajith Kumar U wrote: > >>Hello All, >> >>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >> >>Thanks, >> >>Aju. >> >> >>************************************************** >>Mr.Ajith Kumar U >>Junior Research Fellow, >>Department of Audiology, >>All India Institute of Speech and Hearing, Naimisham Camppus, >>Manasagangothri, >>Mysore,570006 >>INDIA. >>Ph: +91 821 2514449 Ext 186 (O) >> +91 821 2514449 Ext 224 (R) >>Fax: +91 821 2510515 >>Email: ajithajitkumar18(a)rediffmail.com >>************************************************** >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

3 2

Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Hello All, How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? Thanks, Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

2 1

Re: Freesurfer Digest, Vol 28, Issue 32
by Sebastian Moeller 28 Jun '06

28 Jun '06

Hi Anil, On 26. Jun 2006, at 00:08 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 8 > Date: Sun, 25 Jun 2006 17:07:36 -0500 > From: "Anil Roy" <aroy85(a)gmail.com> > Subject: Re: [Freesurfer] recon-all error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <627ebe090606251507s57777571wbd816d66196fc4f5(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative-------------- next part > -------------- > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run > with -force > [root@dhcp-129-105-146-220 freesurfer]# recon-all -force -i > /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects > -all > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force > specified. > Deleting any previous source volumes > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 root root 9126 Jun 25 15:42 > /usr/local/freesurfer/subjects/F200/scripts/recon-all.log > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > WM removal version > /usr/local/freesurfer/subjects/F200 > > mri_convert /root/Desktop/F200.mnc > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > > mri_convert /root/Desktop/F200.mnc > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > reading from /root/Desktop/F200.mnc... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Sun Jun 25 15:42:47 CDT 2006 > Found 1 runs > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > > cp /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > > /usr/local/freesurfer/subjects/F200 > > mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform > > mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform > reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from 4 to 0 (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz... > > mri_add_xform_to_header -c > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm > /usr/local/freesurfer/subjects/F200/mri/orig.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz > > INFO: extension is mgz > #-------------------------------------------- > #@# Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /usr/local/freesurfer/subjects/F200/mri > /usr/local/freesurfer/bin//mri_nu_correct.mni > --i orig.mgz --o nu.mgz --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > Sun Jun 25 15:43:04 CDT 2006 > 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 > tmpdir is ./tmp.mri_nu_correct.mni.3620 > /usr/local/freesurfer/subjects/F200/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc > Can't find the talairach xform > '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm' > Transform is not loaded into mri > reading from orig.mgz... > Talairach transform > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does > not exist ... > Cannot load tal xfm file > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm > 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) > writing to ./tmp.mri_nu_correct.mni.3620/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Sun Jun 25 15:43:10 CDT 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc > ./tmp.mri_nu_correct.mni.3620/nu1.mnc > [root@dhcp-129-105-146-220.speech.northwestern.edu:/usr/local/ > freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] running: > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber > -nokeeptmp -tmpdir /usr/tmp/nu_correct_3670/ > ./tmp.mri_nu_correct.mni.3620/nu0.mnc > ./tmp.mri_nu_correct.mni.3620/nu1.imp > > /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared > libraries: libstdc++.so.5: cannot open shared object file: No such > file or directory Here is the part where it breaks; the freesurfer program you use most likely was compiled with gcc 3.x.x, while FC4 is using gcc 4.x.x. The result from the switch in compilers is that you only have a libstdc++.so.6. If you install the following rpm from your installation medium (or any source from the internet) compat-libstdc++-33-3.2.3-47.fc4.i386; it should work. One caveat, I never used FC4, so I might be way off. Ahoi & good luck Sebastian > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=32512) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=32512) > ERROR: nu_correct > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > > recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006 > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

2 1

Re: [Freesurfer] tesselating
by Chacko Cherian 27 Jun '06

27 Jun '06

yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum. --- Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > and does the filled.mgz look correct? Are the > hemisphere separately > labeled and the cerebellum gone? Also, please post > these to the list so > other people can answer! > > Bruce > > > On Thu, 22 Jun 2006, Chacko Cherian wrote: > > > Yes when I load the image in tkmedit I odnt have > any > > problems.Its perfectly clear and > coronal,horizonatal > > and sagittal are all correct. > > > > --- Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > > >> when you load it in tkmedit does it display > >> properly? That is, is the > >> coronal view really coronal? > >> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> > >>> Hello all, > >>> I ran an Analyze format image in > Fresurfer...just > >> the > >>> Morphometry and reconstruction tutorial..but > found > >>> that it's creating a filled.mgz volume but I'm > >> having > >>> a problem in tesselating and creating the > outputs > >>> lh.orig and rh.orig for the left and right > >>> hemispheres.It displays a very tiny piece of the > >>> volume. > >>> Could you please let me know how to troubleshoot > >> this > >>> problem.. > >>> THanks in advance. > >>> > >>> Chacko. > >>> > >>> > >>> > >>> Chacko Cherian > >>> M.S EE > >>> Graduate Assistant > >>> Department of Psychology > >>> Arizona State University. > >>> Tempe,AZ. > >>> > >>> > >>> > __________________________________________________ > >>> Do You Yahoo!? > >>> Tired of spam? Yahoo! Mail has the best spam > >> protection around > >>> http://mail.yahoo.com > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > > > > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 10

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