Freesurfer September 2005

freesurfer@nmr.mgh.harvard.edu

44 participants
91 discussions

Two questions.
by Clifford A. Smith, PhD 22 Sep '05

22 Sep '05

First, I have successfully completed recon-all on my Mac. I created the subject directories using mksubjdirs prior to running recon-all. After running recon-all the files are all in the mri folder, and the respective folders (eg brain, T1, and filled) remain empty. Is it necessary to build the folders? Second, I would like to use the dti feature in tkmedit. I have the vector and fa volumes calculated with several computer packages in Analyze format. What does tkmedit need to read? A 4d volume with the three vector volumes plus the FA volume? Thanks. ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

2 1

error: TR inconsistent
by agold＠nmr.mgh.harvard.edu 22 Sep '05

22 Sep '05

Hi, Our data is located in /space/kermit/8/users/milad and we had already analyzed this data set with 8 subjects and now are trying to add in 6 new subjects and analyze the final cohort of 14 subjects. During the mkanalysis-sess.new step, we received the following error message: ERROR: /autofs/space/kermit_008/users/milad/ext013d2 has inconsistent TR We checked the seq.info file: [kermit:milad] (nmr-std-env) more ext013d2/bold/seq.info sequencename recall nrows 64 ncols 64 nslcs 45 rowpixelsize 3.125 colpixelsize 3.125 slcpixelsize 3.0000001575331 ntrs 268 TR 3.0000 Turns out that the TR is consistent with the other subjects (i.e., TR = 3), but the slcpixelsize is smaller. It is 8 for all of the other subjects. E.g., see the subject listed below: [kermit:milad] (nmr-std-env) more ext012d1/bold/seq.info sequencename unknown nrows 64 ncols 64 nslcs 45 rowpixelsize 3.125 colpixelsize 3.125 slcpixelsize 8 ntrs 54 TR 3 It's unclear to us whether this is an issue that occurred during data acquisition or preprocessing. How should we go about changing this? Thanks! Andrea -- Andrea Gold Clinical Research Assistant Psychiatric Neuroimaging Research Program Massachusetts General Hospital Phone: (617) 726-5594 Fax: (617) 726-4078 agold2(a)partners.org -- The information transmitted in this email is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

1 0

cortical thickness.
by Moo K. Chung 22 Sep '05

22 Sep '05

> > Hi all, Is the cortical thickness computed as the Euclidean distance from the inner surface toward outer surface or the other way around in FreeSurfer? Thanks. Moo. -- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics University of Wisconsin-Madison

2 1

RE: [Freesurfer] A problem occurred while running recon-all in thenew dev version
by Hsu, Shen-Mou 21 Sep '05

21 Sep '05

Many thanks Nick! It is working now after changing setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin (the default) into setenv MINC_BIN_DIR /home/riobravo/freesurfer/lib/mni/bin (the home directory). Then, I got the latest version of nu_correct. Is there any possibility that my installization went wrong? I reckon that in principle, the MINC tool should be store in the /usr/pubsw/packages/mni/current/bin? thanks again! Shen-Mou -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 9/21/2005 1:14 PM To: Hsu, Shen-Mou Cc: Brian T. Quinn; Freesurfer Mailing List Subject: RE: [Freesurfer] A problem occurred while running recon-all in thenew dev version Hsu, The MINC toolkit is now included in the Freesurfer distribution, and nu_correct should be version 1.10. Since you say that nu_correct returns a version 1.04, its my guess that you have an older version of the MINC toolkit installed somewhere in your path. Remove any setup commands to older MINC toolkits in your .cshrc file. The new $FREESURFER_HOME/FreeSurferEnv.csh script (called by SetUpFreeSurfer.csh) will setup the paths to the newly installed MINC toolkit for you. You can confirm which tools are used by typing: which nu_correct and which nu_estimate_np_and_em These binaries should be in a subdirectory of your new FreeSurfer installation. Also type: echo $PERL5LIB and confirm that the path points to your new installation. Nick On Wed, 2005-09-21 at 13:00 -0400, Hsu, Shen-Mou wrote: > Dear All, > > The problem is fixed as Brian suggested (Thanks Brian), but there is a new problem while running the recon-all. Nu_correct somehow crashes during the proceesing. The follows are the details. Could anyone give me an idea? > > Thanks a lot in advance! > > p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info (1.04). > > [riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 > INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects > Actual FREESURFER_HOME /home/riobravo/freesurfer > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > ######################################## > program versions used > $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > mri_convert --version > $ > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ > minctracc.c > $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ > $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ > $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ > $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ > mri_convert --version > $ > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > Program nu_correct, built from: > Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 > ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ####################################### > GCA RB40_talairach_2005-07-20.gca > AvgCurvTif average.curvature.filled.buckner40.tif > GCS curvature.buckner40.filled.desikan_killiany.gcs > ####################################### > ~/freesurfer/subjects/Sub05 > Using mgz format > --------------------------------------------- > MotionCor Wed Sep 21 10:13:44 EDT 2005 > 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. > /home/riobravo/freesurfer/subjects/Sub05 > mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform > mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform > reading from /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (-1, 0, 0) > Original Data has (1, 1, 1) mm size and (256, 256, 160) 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 /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz... > --------------------------------------------- > Nu Intensity Correction Wed Sep 21 10:14:06 EDT 2005 > mri_convert orig.mgz nu0.mnc > mri_convert orig.mgz nu0.mnc > reading from orig.mgz... > 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 nu0.mnc... > nu_correct -clobber nu0.mnc nu1.mnc > nu_estimate_np_and_em: data directory for package "N3" not found in /home/riobravo/freesurfer/lib/mni/data > [riobravo@localhost.localdomain:/home/riobravo/freesurfer/subjects/Sub05/mri/] [2005-09-21 10:14:18] running: > /usr/pubsw/packages/mni/current/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_7260/ nu0.mnc nu1.imp > > nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) > ERROR: nu_correct > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005 > > > > -----Original Message----- > From: Brian T. Quinn [mailto:btquinn@nmr.mgh.harvard.edu] > Sent: Wed 9/21/2005 10:01 AM > To: Hsu, Shen-Mou > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new dev version > > try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero > padded number such as 001.mgz > > thanks, > brian > > On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote: > > > Hi! > > > > I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out? > > > > Many thanks! > > > > Shen-Mou Hsu > > > > Here are the details. > > > > [riobravo@localhost freesurfer]$ tcsh > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /home/riobravo/freesurfer > > FSFAST_HOME /home/riobravo/freesurfer/fsfast > > SUBJECTS_DIR /home/riobravo/freesurfer/subjects > > FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions > > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > PERL5LIB > > GSL_DIR /home/riobravo/freesurfer/lib/gsl > > QTDIR /home/riobravo/freesurfer/lib/qt > > TCLLIBPATH /home/riobravo/freesurfer/lib/tcltktixblt/lib > > FSL_DIR /home/riobravo/fsl > > > > riobravo@localhost orig]$ mri_convert /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz > > [riobravo@localhost orig]$ ls > > Sub05.mgz > > > > riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 > > INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects > > Actual FREESURFER_HOME /home/riobravo/freesurfer > > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > > ######################################## > > program versions used > > $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ > > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > > mri_convert --version > > $ > > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ > > minctracc.c > > $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ > > $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ > > $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ > > $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ > > mri_convert --version > > $ > > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > > Program nu_correct, built from: > > Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 > > ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > > ####################################### > > GCA RB40_talairach_2005-07-20.gca > > AvgCurvTif average.curvature.filled.buckner40.tif > > GCS curvature.buckner40.filled.desikan_killiany.gcs > > ####################################### > > ~/freesurfer/subjects/Sub05 > > Using COR format > > --------------------------------------------- > > MotionCor Wed Sep 21 09:51:01 EDT 2005 > > ERROR: no data found in /home/riobravo/freesurfer/subjects/Sub05/mri/orig > > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > > recon-all exited with errors at Wed Sep 21 09:51:01 EDT 2005 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

2 1

head points
by Don Hagler 21 Sep '05

21 Sep '05

Can anyone supply an example head points file for use with tkmedit?

1 0

RE: [Freesurfer] A problem occurred while running recon-all in the new dev version
by Hsu, Shen-Mou 21 Sep '05

21 Sep '05

Dear All, The problem is fixed as Brian suggested (Thanks Brian), but there is a new problem while running the recon-all. Nu_correct somehow crashes during the proceesing. The follows are the details. Could anyone give me an idea? Thanks a lot in advance! p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info (1.04). [riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using mgz format --------------------------------------------- MotionCor Wed Sep 21 10:13:44 EDT 2005 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. /home/riobravo/freesurfer/subjects/Sub05 mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform reading from /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 160) 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 /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz... --------------------------------------------- Nu Intensity Correction Wed Sep 21 10:14:06 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... 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 nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc nu_estimate_np_and_em: data directory for package "N3" not found in /home/riobravo/freesurfer/lib/mni/data [riobravo@localhost.localdomain:/home/riobravo/freesurfer/subjects/Sub05/mri/] [2005-09-21 10:14:18] running: /usr/pubsw/packages/mni/current/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_7260/ nu0.mnc nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005 -----Original Message----- From: Brian T. Quinn [mailto:btquinn@nmr.mgh.harvard.edu] Sent: Wed 9/21/2005 10:01 AM To: Hsu, Shen-Mou Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new dev version try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero padded number such as 001.mgz thanks, brian On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote: > Hi! > > I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out? > > Many thanks! > > Shen-Mou Hsu > > Here are the details. > > [riobravo@localhost freesurfer]$ tcsh > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/riobravo/freesurfer > FSFAST_HOME /home/riobravo/freesurfer/fsfast > SUBJECTS_DIR /home/riobravo/freesurfer/subjects > FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > PERL5LIB > GSL_DIR /home/riobravo/freesurfer/lib/gsl > QTDIR /home/riobravo/freesurfer/lib/qt > TCLLIBPATH /home/riobravo/freesurfer/lib/tcltktixblt/lib > FSL_DIR /home/riobravo/fsl > > riobravo@localhost orig]$ mri_convert /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz > [riobravo@localhost orig]$ ls > Sub05.mgz > > riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 > INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects > Actual FREESURFER_HOME /home/riobravo/freesurfer > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > ######################################## > program versions used > $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > mri_convert --version > $ > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ > minctracc.c > $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ > $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ > $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ > $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ > mri_convert --version > $ > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > Program nu_correct, built from: > Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 > ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 > ####################################### > GCA RB40_talairach_2005-07-20.gca > AvgCurvTif average.curvature.filled.buckner40.tif > GCS curvature.buckner40.filled.desikan_killiany.gcs > ####################################### > ~/freesurfer/subjects/Sub05 > Using COR format > --------------------------------------------- > MotionCor Wed Sep 21 09:51:01 EDT 2005 > ERROR: no data found in /home/riobravo/freesurfer/subjects/Sub05/mri/orig > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux > recon-all exited with errors at Wed Sep 21 09:51:01 EDT 2005 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn

2 1

A problem occurred while running recon-all in the new dev version
by Hsu, Shen-Mou 21 Sep '05

21 Sep '05

Hi! I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out? Many thanks! Shen-Mou Hsu Here are the details. [riobravo@localhost freesurfer]$ tcsh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/riobravo/freesurfer FSFAST_HOME /home/riobravo/freesurfer/fsfast SUBJECTS_DIR /home/riobravo/freesurfer/subjects FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB GSL_DIR /home/riobravo/freesurfer/lib/gsl QTDIR /home/riobravo/freesurfer/lib/qt TCLLIBPATH /home/riobravo/freesurfer/lib/tcltktixblt/lib FSL_DIR /home/riobravo/fsl riobravo@localhost orig]$ mri_convert /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz [riobravo@localhost orig]$ ls Sub05.mgz riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using COR format --------------------------------------------- MotionCor Wed Sep 21 09:51:01 EDT 2005 ERROR: no data found in /home/riobravo/freesurfer/subjects/Sub05/mri/orig Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 09:51:01 EDT 2005

2 1

newbie question regarding pooling (analysis over different sessions)
by Sebastian Moeller 20 Sep '05

20 Sep '05

Dear fs-fast wizards, doing monkey fMRI in Bremen (block desing so far) I run into the problem that analysing the data from one session does not lead to well defined activation maps. Therefore I would like to pool over several sessions (always within one subject). Unfortunately I have did not manage to always position the slices at the same position, I recorded a different number of runs each session. Now my assumption is all I need to do is define according df and sf files and be done with. But at what stage (mc-sess, spatialsmooth-sess, mkanalysis-sess.new, selxavg-sess, mkcontrast-sess or stxgrinfer-sess)? Is it advisable to motion correct all session runs together, or combine the data after that step? So excuse me for my uneducated question, but I would be delighted to tap into this list's vast knowledge before debarking into computationally long experiments. One more question, is it necessary/helpful to record low-res anatomicals before functional runs to register separate sessions, or is this step avoidable. Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 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

5 6

Atlases and newer releases
by Satrajit Ghosh 20 Sep '05

20 Sep '05

Does one need to recreate custom atlases when changing to a new release? And if so does this process imply reprocessing all the subjects originally used to create the atlas? Thanks, Satra

2 1

RE: [Freesurfer] Autorecon re-processing
by Fornito, Alexander 20 Sep '05

20 Sep '05

Would manually changing the intensities in brain volume using the configure volume brush tool in tkmedit help? Shoudl white matter be re-labelled as 255? What would be a good value for grey matter? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 9/20/2005 2:19 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Autorecon re-processing probably susceptibility problems. Try putting some control points in the wm, but there may not be enough g/w contrast to get good surfaces. On Tue, 20 Sep 2005, Fornito, Alexander wrote: > > Sorry, I missed it - forgive my absent mindedness :( > > Onto a more valid problem (I hope!), I've had trouble segmenting the olfactory sulcus on some of my images. The wm wolume seems to segment well, but the orig and/or white surface doesn't follow this. Rather than enter the olfacoty sulcus, only partially enters it. I was curious as to why the orig/white surface would not follow the surface of the wm volume, and if there is anyway to fix it? > Thanks, > Alex > > -----Original Message----- > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tue 9/20/2005 4:03 AM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Autorecon re-processing > > does your version not tell you these things when you run -help? > > > > Fornito, Alexander wrote: > >> HI, >> Just wanted to check a few things re: re-running autorecon. >> I'm guessing that re-running autorecon with the -pial flag re-runs make_final_surfaces, which takes about 4-6 hours (correct?). >> What is re-run when the -wm and -cp flags are used, and how long do they take? >>> From what I understand, -cp would require re-running everything from intensity normalization on, including the subcortical segmentation, while -wm would require re-running the topology fixer and final surfaces. >> Does this sound about right? >> Thanks, >> Alex >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > >

2 1

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Freesurfer September 2005