Freesurfer

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30129 discussions

recon-all
by Sasha Wolosin 08 Sep '05

08 Sep '05

I am having some trouble running recon-all. one thing I have observed: Freesurfer keeps searching in the /mri folder instead of the /mri/orig folder, for example, in order to run tkmedit I had to type the command as follows: tkmedit 2332 orig/orig.mgz and I had to copy the orig.mgz file from the /mri/orig folder to the /mri folder in order to run recon-all, otherwise I would get an error during the 'Nu Intensity Correction' step. Is this what it is supposed to do? I still get an error during the mri_normalize step (see below- the error is all the way at the end) Do you know what I might be missing? Thanks, Sasha [wolosin@localhost mri]# recon-all -subjid 2332 -autorecon1 -mgz INFO: SUBJECTS_DIR is /home/wolosin/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- MotionCor Thu Sep 8 16:34:35 EDT 2005 INFO: no runs were found in /home/wolosin/subjects/2332/mri, however, there is a volume /home/wolosin/subjects/2332/mri/rawavg.mgz, so I am just going to proceed with that as the input. --------------------------------------------- Nu Intensity Correction Thu Sep 8 16:34:38 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:41] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 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_ 1646/ nu0.mnc nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 22 CV of field change: 0.00094628 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:58] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu0.mnc /us r/tmp/nu_correct_1646//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu1.mnc nu2.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:01] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 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_ 1951/ nu1.mnc nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 12 CV of field change: 0.000947063 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:10] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu1.mnc /us r/tmp/nu_correct_1951//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu2.mnc nu3.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:13] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 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_ 2142/ nu2.mnc nu3.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 9 CV of field change: 0.000974347 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:20] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu2.mnc /us r/tmp/nu_correct_2142//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu3.mnc nu4.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:23] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 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_ 2295/ nu3.mnc nu4.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 8 CV of field change: 0.000890052 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:30] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu3.mnc /us r/tmp/nu_correct_2295//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done mri_convert nu4.mnc nu.mgz mri_convert nu4.mnc nu.mgz reading from nu4.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mgz... --------------------------------------------- Talairach Thu Sep 8 16:35:36 EDT 2005 /home/wolosin/subjects/2332/mri talairach2 2332 .mgz INFO: registering 2332 Thu Sep 8 16:35:36 EDT 2005 -------------------------------------------- mri_convert nu.mgz nu.mnc mri_convert nu.mgz nu.mnc reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm nu.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /home/wolosin/subjects/2332/mri/transforms/talairach.xfm /home/wolosin/subjects/2332/mri/orig.mgz /home/wolosin/subjects/2332/mri/orig.m gz INFO: extension is mgz Thu Sep 8 16:36:16 EDT 2005 --------------------------------------------- Intensity Normalization Thu Sep 8 16:36:16 EDT 2005 /home/wolosin/subjects/2332/mri mri_normalize nu.mgz T1.mgz reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Sep 8 16:37:02 EDT 2005 Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. 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1 0

image output question
by Tracy Wang 08 Sep '05

08 Sep '05

Hi all, is there anyway to change space of the images from 256 x 256 x 256 (in my case in minc format) to output to 172 x 220 x 156? Thanks! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

1 0

recon-all
by Keyma Prince 08 Sep '05

08 Sep '05

Hello, I tried running one of my subjects through the whole autorecon stream and I noticed more of the basal ganglia region was filled in then was described in the previous tutorial. Is this extra filling ok? The data I ran it on is located in /space/engram/11/users/rk_fmri_struc/Y24_010705a_STRUC. Thanks, Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

2 1

Intstallation problems on new dev?
by Fornito, Alexander 08 Sep '05

08 Sep '05

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the $FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I source the environment, I get: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer-dev20050905 FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni/lib PERL5LIB /usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5 GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl QTDIR /usr/local/freesurfer-dev20050905/lib/qt TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl However, when I try to run autorecon, I get a message saying "cmd: Undefined variable." I get this whether the environment is set to link to perl5 in $FREESURFER_HOME/lib/mni/lib/ or in /usr/pubsw/packages/mni/current/lib/. I don't even know if it's the perl library that's the problem. Could someone please help out? As far as we're aware, all the environments are set correctly, so we're not sure what Undefined variable is referring to. The entire output is below: recon-all -autorecon1 -subjid 27_new -hemi lh INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $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@martinos01 (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### /data/flanders/work/alex/freesurfer/subjects/27_new Using COR format --------------------------------------------- MotionCor Thu Sep 8 11:59:54 EST 2005 INFO: no runs were found in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX, however, there is a volume in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig, so I am just going to proceed with that as the input. cmd: Undefined variable.

5 4

RE: [Freesurfer] Intstallation problems on new dev?
by Fornito, Alexander 08 Sep '05

08 Sep '05

Seems to be working now. Thanks Doug, you're a lifesaver!! As an aside, will surfaces created using the 20050509 dev version be compatible with those created using the upcoming stable release? -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/8/2005 1:43 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? That's due to a problem I created a few days ago. Fixes are at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve doug On Thu, 8 Sep 2005, Fornito, Alexander wrote: > Hi, > We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the $FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I source the environment, I get: > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer-dev20050905 > FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast > SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects > FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions > MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin > MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni/lib > PERL5LIB /usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5 > GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl > QTDIR /usr/local/freesurfer-dev20050905/lib/qt > TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib > FSL_DIR /usr/local/fsl > > However, when I try to run autorecon, I get a message saying "cmd: Undefined variable." I get this whether the environment is set to link to perl5 in $FREESURFER_HOME/lib/mni/lib/ or in /usr/pubsw/packages/mni/current/lib/. > I don't even know if it's the perl library that's the problem. Could someone please help out? As far as we're aware, all the environments are set correctly, so we're not sure what Undefined variable is referring to. The entire output is below: > > recon-all -autorecon1 -subjid 27_new -hemi lh > INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 > Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux > ######################################## > program versions used > $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > mri_convert --version > $ > $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ > minctracc.c > $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ > $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ > $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ > $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ > mri_convert --version > $ > # $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@martinos01 (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40 > ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > ####################################### > GCA RB40_talairach_2005-07-20.gca > AvgCurvTif average.curvature.filled.buckner40.tif > GCS curvature.buckner40.filled.desikan_killiany.gcs > ####################################### > /data/flanders/work/alex/freesurfer/subjects/27_new > Using COR format > --------------------------------------------- > MotionCor Thu Sep 8 11:59:54 EST 2005 > > INFO: no runs were found in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX, > however, there is a volume in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig, > so I am just going to proceed with that as the input. > cmd: Undefined variable. > > > _______________________________________________ > 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

2 1

talairach transform problem
by Michele Perry 07 Sep '05

07 Sep '05

I ran recon-all -stage1 -nomotioncor -subjid <subjectID> It exited with errors during mri_fill: mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... I ran -stage1 again with rh, lh, cc, and pons seed points. It finished without errors but the cc cut was still incorrect (wm in the rh was incorrectly labelled lh wm). I opened "brain" in tkmedit and loaded the talairach transform. The talairach is really off. When I choose "corornal" view, I get horizonal view. Increasing slice numbers go superior to inferior When I choose "horizontal" view, I get an upside-down coronal view, increasing slice numbers go anterior to posterior When I choose "sagittal" view, I get a sagittal view rotated 90 degrees counter-clockwise. Increasing slice numbers go right to left. How do I fix this?

3 2

new 'dev' release for Linux rh9, centos4 and centos4_x86_64
by Nick Schmansky 07 Sep '05

07 Sep '05

Freesurfer community, For those who wish to install a 'development' release of Freesurfer on Linux RedHat 9, CentOS 4 or CentOS 4 x86_64 platforms, distribution files are now posted at: http://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D On this distribution site, a README is available: freesurfer-Linux-platform-dev20050905-full.README.txt The new distributions include: freesurfer-Linux-rh9-dev20050905-full.tar.gz freesurfer-Linux-centos4-dev20050905-full.tar.gz freesurfer-Linux-centos4_x86_64-dev20050905-full.tar.gz The 'dev' release contains all the functionality of the upcoming 'stable' release, but has not been fully tested, particularly in regards to installation issues. This 'dev' release is intended for those who wish to attempt an installation on their Linux platform, and are willing to give feedback on possible installation problems. This 'dev' release contains most of the libraries that Freesurfer requires: the MINC toolkit, Tcl/Tk/Tix and BLT libraries, GSL and Qt, as well as sample MRI data. The release may be installed in any directory. A Mac OS X 'dev' build is not available just yet. Please direct comments or questions to this mailing list.

2 4

segmentation fault during make_average_surface
by Marie Schaer 07 Sep '05

07 Sep '05

Hello, I'm trying to make an average surface using the latest version of make_average_surface (2005/08/02 19:14:20 nicks Exp), and I got the same error as posted in the following message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01135.html, with a segmentation fault when mris_average_surface is called (I get the same segmentation fault when running mris_average_surface alone): mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_test subj1 subj2 processing subject subj1... The following must be revisited******************************************* Segmentation fault I did not find in the mailing list how to solve this, thank you very much for your help, Marie Schaer

1 0

RE: [Freesurfer] mri_convert with *.IMG
by Thomas, Adam (NIH/NIMH) 06 Sep '05

06 Sep '05

Hi Michele, It might not be the most direct way of converting your data to COR format, but AFNI has a good utility for dealing with GE data: http://afni.nimh.nih.gov/pub/dist/doc/program_help/Ifile.html Then you can use mri_convert to get from AFNI to COR format. Here's an example: [antimony:07129] (nmr-dev-env) ls 008 I.001 I.014 I.027 I.040 I.053 I.066 I.079 I.092 I.105 I.118 I.002 I.015 I.028 I.041 I.054 I.067 I.080 I.093 I.106 I.119 I.003 I.016 I.029 I.042 I.055 I.068 I.081 I.094 I.107 I.120 I.004 I.017 I.030 I.043 I.056 I.069 I.082 I.095 I.108 I.121 I.005 I.018 I.031 I.044 I.057 I.070 I.083 I.096 I.109 I.122 I.006 I.019 I.032 I.045 I.058 I.071 I.084 I.097 I.110 I.123 I.007 I.020 I.033 I.046 I.059 I.072 I.085 I.098 I.111 I.124 I.008 I.021 I.034 I.047 I.060 I.073 I.086 I.099 I.112 SERHDR.008 I.009 I.022 I.035 I.048 I.061 I.074 I.087 I.100 I.113 I.010 I.023 I.036 I.049 I.062 I.075 I.088 I.101 I.114 I.011 I.024 I.037 I.050 I.063 I.076 I.089 I.102 I.115 I.012 I.025 I.038 I.051 I.064 I.077 I.090 I.103 I.116 I.013 I.026 I.039 I.052 I.065 I.078 I.091 I.104 I.117 [antimony:07129] (nmr-dev-env) Ifile 008/I.* ++ using time stamp. ++ using slice pattern alt+z ++ using output directory afni ++ Expanding file list ... ++ found 124 '*/I.*' files ++ Scanning GE headers ++ 124 files are good images ++ File time threshold = 10 s RUN 01: 008/I.001 .. 008/I.124 124 images 1 Volume(s) Found 1 complete scans. Run GERT_Reco to create AFNI bricks. [antimony:07129] (nmr-dev-env) ./GERT_Reco Will use OutBrick_r1 for this data set. Forming image list ... >From 008/I.001 ... to 008/I.124 Done with File List. on to To3D ... Now Running: to3d -save_outliers OutBrick_r1_Outliers.1D -epan -prefix OutBrick_r1 -time:zt 124 1 0 alt+z -@ < ./PangaList to3d: 2D slices into 3D datasets for AFNI, by RW Cox ++ WARNING: TR expressed in milliseconds will be converted to TR=0.000000s Illegal value of nt after -time: option Counting images: total=124 2D slices Reading images: ......................................... 3D dataset written to disk Done with To3D. READY. \012Either execute: cd afni afni & Or <rescan this> in afni [antimony:07129] (nmr-dev-env) ls afni/ OutBrick_r1+orig.BRIK OutBrick_r1+orig.HEAD [antimony:07129] (nmr-dev-env) mkdir COR [antimony:07129] (nmr-dev-env) mri_convert afni/OutBrick_r1+orig.BRIK COR/ mri_convert afni/OutBrick_r1+orig.BRIK COR/ reading from afni/OutBrick_r1+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 124) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (-126.031197, -122.851402, -46.322140) DELTA : (0.937500, 0.937500, 1.000000) IDCODE_STRING : XYZ_2zCmhd23DSvVbCOGq0klwg BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 668.000000 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.000000 ==================================================================== BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 668.000000 <--> actual max = 668.000000 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 (0.9375, 0.9375, 1) mm size and (256, 256, 124) 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 COR/... [antimony:07129] (nmr-dev-env) Hope that helps, -a --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 -----Original Message----- From: Michele Perry [mailto:mperry@ucsd.edu] Sent: Thursday, September 01, 2005 5:35 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert with *.IMG Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have tried to convert from .IMG to COR using mri_convert -it <see below> -ot cor /path/001.IMG $SUBJECTS_DIR/subjid/mri/orig Here's what I get... -it anaylze -ot cor (I get errors if I don't give an output type) (result: reading from /path/001.IMG... analyzeRead(): cannot find any files for /path/001.IMG) -it ge -ot cor (result: reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG) -it gelx -ot cor reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG I have tried running this with the .IMG files in their own separate directory and in a directory with the .HDRs and .TIFs. I've also tried running it without specifing the .IMG file, just the directory. Any ideas what I'm doing wrong? Michele _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

recon-all problem
by Paul Aparicio 06 Sep '05

06 Sep '05

Hello all, I run recon-all and get this problem: --------------------------------------------- Nu Intensity Correction Tue Sep 6 13:04:59 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, -0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/pubsw/packages/perl/5.6.0/lib/5.6.0/i686-l inux /usr/pubsw/packages/perl/5.6.0/lib/5.6.0 /usr/pubsw/packages/perl/5.6.0/lib/site_perl/5.6.0/i6 86-linux /usr/pubsw/packages/perl/5.6.0/lib/site_perl/5.6.0 /usr/pubsw/packages/perl/5.6.0/lib/site _perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct Anyone know how I might fix this? Thanks!

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