Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

Talairach Failure
by Andrew Jahn 10 Apr '09

10 Apr '09

Hi, I got the following error when trying to run recon-all on an MP-RAGE T1-weighted image: Fri Apr 10 16:25:01 EDT 2009 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Fri Apr 10 16:25:02 EDT 2009 /usr/local/freesurfer/subjects/MPRAGE/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Darwin The-Ohio-State-University-Server.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 And this was the command I typed: recon-all -subject MPRAGE -i fmprage.nii -all auto-recon works for other T1's using a FLASH sequence, for example, but failed on this one. Any help would be greatly appreciated. Thank you! -Andrew

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removing background
by slew＠nmr.mgh.harvard.edu 10 Apr '09

10 Apr '09

Hi, I want to remove the background 0 in the segmented volume like aseg.mgz, and saved the volume without the background. What is the simplest way to do it? Best, Seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging
by Christine Fennema Notestine 10 Apr '09

10 Apr '09

Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging Department of Psychiatry, University of California, San Diego The Department of Psychiatry at the University of California, San Diego is pleased to invite applications for a postdoctoral research scholar position in behavior genetics and neuroimaging under the direction of Drs. William Kremen (Psychiatry) and Anders Dale (Radiology and Neuroscience). The position focuses on training in the application of sophisticated psychometric techniques (particularly twin analyses) and neuroimaging methods (structural MRI , DTI, fMRI, and ASL) that will be applied to the NIH/NIA-funded Vietnam Era Twin Study of Aging (VETSA) in collaboration with investigators at Boston University, Massachusetts General Hospital, and Virginia Commonwealth University. VETSA is a unique longitudinal study of over 600 middle-aged male twin pairs that focuses on understanding cognitive and brain aging. Over 500 twins have undergone 3D structural MRI and DTI in VETSA wave 1. These twins also underwent extensive neurocognitive assessment, personality and psychosocial measures, a medical history interview, in-lab physical health measures such as blood pressure and pulmonary function, and hormonal assays for cortisol, testosterone, and DHEAS. DNA has been obtained from all subjects and, to date, they have been genotyped for APOE. Genome-wide genotyping of all VETSA subjects is planned. Wave 2 of the project, which was recently funded, will acquire five-year follow-up data, and also include fMRI and ASL scans. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Requirements for the position are: 1) completion of relevant Ph.D. research activities within the past five years; 2) advanced writing and advanced statistical or neuroimaging skills, and 3) an interest in imaging genetics research. Experience with multilevel data analysis, twin modeling, genetics, and/or neuroimaging is desirable. The postdoctoral candidate will be encouraged to develop his or her own research projects that fit within the overall scope of the project. The position will entail immersion in twin modeling (e.g., using Mx software) and MR image analysis including FreeSurfer and other methods. This advertisement is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send a copy of your CV, a brief statement of research interests and goals, and any selected reprints to the address below. Letters of reference will be required before final approval of hiring. Informal inquiries concerning this position are encouraged. Please e-mail wkremen(a)ucsd.edu for more details. William S. Kremen, Ph.D. Department of Psychiatry University of California, San Diego 9500 Gilman Drive (MC 0738) La Jolla, CA 92093-0738 -- Christine Fennema Notestine, Ph.D. Asst Professor of Psychiatry and Radiology University of California, San Diego Phone: 858-822-3198 / 858-246-0605 E-mail: fennema(a)ucsd.edu Fax: 858-534-1078

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Dense annotations
by Alex Fornito 09 Apr '09

09 Apr '09

Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file. Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes. Does this limit have something to do with what is specified in the colortable.orig_tab structure? We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else? Thanks for your help, Alex -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af397(a)cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: fornitoa(a)unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469

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mri_glmfit
by Lusineh Gharapetian 08 Apr '09

08 Apr '09

Hello, I'm trying to use the mri_glmfit function but keep running into the same error. I am using the FSGD format and have set up my fsgd file according to the tutorial instructions: " GroupDescriptorFile 1 Title mci_age_BNTchange Class Male Class Female Variables Age BNTchange Input Subject1 Male 70 2 Input Subject2 Female 75 -3 Input Subject3 Female 72 0 etc." Our .mat file states: " 0 0 0 1" indicating that "BNTchange" is our variable of interest. We are attempting to run a DOSS analysis. The line of code I type into the terminal is: " mri_glmfit --glmdir mci_age_bntchange_lh --y dv-visit2-lh.mgz --fgd mci_age_bntchange.fsgd doss --C mci_age_bntchange.mat" This results in the following error: "ERROR: matrix is illconditioned or badly scaled, condno = 1e+08" We have tried runninf this off of different versions of Freesurfer (R302 and R305) and cannot figure out how to fix this error. Any help would be appreciated! Thanks! - Lusineh Gharapetian

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Md5sum download mismatch
by john.dornisch＠scra.org 08 Apr '09

08 Apr '09

Hello, I am having a problem downloading the latest version of freesurfer 4.3. On 2 separate servers on 2 separate days I get the same md5sum which does not match the md5sums listed in the md5sum file in the downloads section. your md5s 29450bd531d94909cc858384551d43b0 freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz df4c679702d3bf01c458276a93a90547 freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz My md5sums 54de93353546c88ed9dc7b9de0b2384d freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz 6da2363ffc42e9c65a22033ad057748c freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz Please advise. Thanks John Dornisch

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mri_ca_train parameters?
by Jamie Hanson 08 Apr '09

08 Apr '09

Hi Freesufer folks- I was just about to start constructing a custom aseg atlas and I wondered if there were any recommendations for any of the optional flags? Any parameters yield better results (especially for specific brain regions)? I was focused on improving amygdala segmentation for my structural images (hence my asking). Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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RES: [Freesurfer] libvtkpng.so.5.2 missing?
by Pedro Paulo de Magalhaes Oliveira Junior 08 Apr '09

08 Apr '09

run yum list | grep vtk | grep png Sent from my Nokia phone @E71 -----Msg original----- De: Derin Cobia Enviada: 08/04/2009 15:56:27 Assunto: [Freesurfer] libvtkpng.so.5.2 missing? We're running subjects under the new 4.3.0 version (CentOS 4 platform), and are experiencing the following error during the cortical ribbon mask stage: -------------------------------------------------------------------------------------------- #@# Cortical ribbon mask Wed Apr 8 07:12:20 CDT 2009 /disk/NIACAL/human/freesurfer/conte_mprage_v4.3/020319_2263/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon -- save_distance 020319_2263 mris_volmask.bin: error while loading shared libraries: libvtkpng.so. 5.2: cannot open shared object file: No such file or directory Linux heinz 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Apr 8 07:12:21 CDT 2009 -------------------------------------------------------------------------------------------- It appears that libvtkpng.so.5.2 does indeed not exist (in fact, no libvtkpng* files were found) in ~/freesurfer/lib/vtk/lib/vtk-5.2 for the current 4.3.0 CentOS 4 (32-bit) distribution we have, but found them present in our 4.1.0 (32-bit) and 4.3.0 (64-bit) distros . This may just be a case of "the missing libraries," but are they supposed to be gone? If not, are we safe to just copy them into the 4.3.0 vtk dir as a short term fix? Thanks. -Derin _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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libvtkpng.so.5.2 missing?
by Derin Cobia 08 Apr '09

08 Apr '09

We're running subjects under the new 4.3.0 version (CentOS 4 platform), and are experiencing the following error during the cortical ribbon mask stage: -------------------------------------------------------------------------------------------- #@# Cortical ribbon mask Wed Apr 8 07:12:20 CDT 2009 /disk/NIACAL/human/freesurfer/conte_mprage_v4.3/020319_2263/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon -- save_distance 020319_2263 mris_volmask.bin: error while loading shared libraries: libvtkpng.so. 5.2: cannot open shared object file: No such file or directory Linux heinz 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Apr 8 07:12:21 CDT 2009 -------------------------------------------------------------------------------------------- It appears that libvtkpng.so.5.2 does indeed not exist (in fact, no libvtkpng* files were found) in ~/freesurfer/lib/vtk/lib/vtk-5.2 for the current 4.3.0 CentOS 4 (32-bit) distribution we have, but found them present in our 4.1.0 (32-bit) and 4.3.0 (64-bit) distros . This may just be a case of "the missing libraries," but are they supposed to be gone? If not, are we safe to just copy them into the 4.3.0 vtk dir as a short term fix? Thanks. -Derin

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v 1.20 asegstats2table bug
by Victoria Williams 08 Apr '09

08 Apr '09

Hello, I am having a bit of trouble using asegstats2table. I have tried using different versions of this command and if only I could combine the two, it would work perfectly. I am trying to compile wmparc stats for about 160 subjects. Unlike the new aparcstats2table, asegstats2table seems to not have the capacity to only report segmentations common to all subjects. Therefore, I end up with about 160 subjects with unmatching columns in the table. The first version of asegstats2table I tried was v 1.8 in my stable4 environment. This version allowed me to specify the --statsfile as wmparc.stats. However, I could not exclude segmentations such as the wm-hypointensities that was not common to all subjects and was messing up my table. The newer 1.20 version in the dev environment does let me specify --no-segno, however it is not recognizing the --statsfile flag although it is mentioned in the usage, and gives the following error: leia:tori:~[82] asegstats2table --version $Id: asegstats2table,v 1.20 2009/04/07 18:18:09 krish Exp $ leia:tori:CVRAM[87] asegstats2table --subjects CVRAM_001_recon CVRAM_002_recon CVRAM_003_recon CVRAM_004_recon CVRAM_005_recon CVRAM_006_recon CVRAM_007_recon CVRAM_008_recon CVRAM_009_recon CVRAM_010_recon CVRAM_011_recon CVRAM_012_recon CVRAM_013_recon CVRAM_014_recon CVRAM_016_recon CVRAM_017_recon CVRAM_018_recon CVRAM_019_recon CVRAM_020_recon CVRAM_021_recon CVRAM_022_recon CVRAM_023_recon CVRAM_024_recon CVRAM_025_recon CVRAM_026_recon CVRAM_027_recon CVRAM_028_recon CVRAM_029_recon CVRAM_030_recon CVRAM_031_recon CVRAM_032_recon CVRAM_033_recon CVRAM_034_recon CVRAM_035_recon CVRAM_036_recon CVRAM_037_recon CVRAM_038_recon CVRAM_040_recon CVRAM_041_recon CVRAM_042_recon CVRAM_043_recon CVRAM_044_recon CVRAM_045_recon CVRAM_046_recon CVRAM_047_recon CVRAM_048_recon CVRAM_050_recon CVRAM_051_recon CVRAM_052_recon CVRAM_053_recon CVRAM_054_recon CVRAM_055_recon CVRAM_057_recon CVRAM_058_recon CVRAM_059_recon CVRAM_060_recon CVRAM_061_recon CVRAM_062_recon CVRAM_063_recon CVRAM_064_recon CVRAM_066_recon CVRAM_067_recon CVRAM_068_recon CVRAM_069_recon CVRAM_070_recon CVRAM_072_recon CVRAM_073_recon CVRAM_074_recon CVRAM_075_recon CVRAM_076_recon CVRAM_077_recon CVRAM_078_recon CVRAM_079_recon CVRAM_080_recon CVRAM_081_recon CVRAM_082_recon CVRAM_083_recon CVRAM_084_recon CVRAM_085_recon CVRAM_086_recon CVRAM_087_recon CVRAM_089_recon CVRAM_090_recon CVRAM_091_recon CVRAM_092_recon CVRAM_093_recon CVRAM_095_recon CVRAM_096_recon CVRAM_097_recon CVRAM_098_recon CVRAM_099_recon CVRAM_100_recon CVRAM_101_recon CVRAM_103_recon CVRAM_104_recon CVRAM_1045_recon CVRAM_1046_recon CVRAM_105_recon CVRAM_106_recon CVRAM_108_recon CVRAM_109_recon CVRAM_111_recon CVRAM_112_recon CVRAM_113_recon CVRAM_114_recon CVRAM_115_recon CVRAM_117_recon CVRAM_118_recon CVRAM_119_recon CVRAM_120_recon CVRAM_121_recon CVRAM_122_recon CVRAM_124_recon CVRAM_125_recon CVRAM_126_recon CVRAM_127_recon CVRAM_128_recon CVRAM_129_recon CVRAM_130_recon CVRAM_131_recon CVRAM_132_recon CVRAM_133_recon CVRAM_135_recon CVRAM_136_recon CVRAM_138_recon CVRAM_139_recon CVRAM_140_recon CVRAM_142_recon CVRAM_143_recon CVRAM_144_recon CVRAM_145_recon CVRAM_146_recon CVRAM_147_recon CVRAM_148_recon CVRAM_149_recon CVRAM_151_recon CVRAM_152_recon CVRAM_153_recon CVRAM_154_recon CVRAM_155_recon CVRAM_156_recon CVRAM_157_recon CVRAM_158_recon CVRAM_159_recon --no-segno 77 78 79 80 81 82 --subdir stats --statsfile wmparc-nonzero.stats --tablefile STATS2/stats_tables-cvram/WMparc_stats_nonzero_04082009.txt asegstats2table: error: no such option: --statsfile I also tried this: leia:tori:CVRAM[88] asegstats2table --subjects CVRAM_001_recon CVRAM_002_recon CVRAM_003_recon CVRAM_004_recon CVRAM_005_recon CVRAM_006_recon CVRAM_007_recon CVRAM_008_recon CVRAM_009_recon CVRAM_010_recon CVRAM_011_recon CVRAM_012_recon CVRAM_013_recon CVRAM_014_recon CVRAM_016_recon CVRAM_017_recon CVRAM_018_recon CVRAM_019_recon CVRAM_020_recon CVRAM_021_recon CVRAM_022_recon CVRAM_023_recon CVRAM_024_recon CVRAM_025_recon CVRAM_026_recon CVRAM_027_recon CVRAM_028_recon CVRAM_029_recon CVRAM_030_recon CVRAM_031_recon CVRAM_032_recon CVRAM_033_recon CVRAM_034_recon CVRAM_035_recon CVRAM_036_recon CVRAM_037_recon CVRAM_038_recon CVRAM_040_recon CVRAM_041_recon CVRAM_042_recon CVRAM_043_recon CVRAM_044_recon CVRAM_045_recon CVRAM_046_recon CVRAM_047_recon CVRAM_048_recon CVRAM_050_recon CVRAM_051_recon CVRAM_052_recon CVRAM_053_recon CVRAM_054_recon CVRAM_055_recon CVRAM_057_recon CVRAM_058_recon CVRAM_059_recon CVRAM_060_recon CVRAM_061_recon CVRAM_062_recon CVRAM_063_recon CVRAM_064_recon CVRAM_066_recon CVRAM_067_recon CVRAM_068_recon CVRAM_069_recon CVRAM_070_recon CVRAM_072_recon CVRAM_073_recon CVRAM_074_recon CVRAM_075_recon CVRAM_076_recon CVRAM_077_recon CVRAM_078_recon CVRAM_079_recon CVRAM_080_recon CVRAM_081_recon CVRAM_082_recon CVRAM_083_recon CVRAM_084_recon CVRAM_085_recon CVRAM_086_recon CVRAM_087_recon CVRAM_089_recon CVRAM_090_recon CVRAM_091_recon CVRAM_092_recon CVRAM_093_recon CVRAM_095_recon CVRAM_096_recon CVRAM_097_recon CVRAM_098_recon CVRAM_099_recon CVRAM_100_recon CVRAM_101_recon CVRAM_103_recon CVRAM_104_recon CVRAM_1045_recon CVRAM_1046_recon CVRAM_105_recon CVRAM_106_recon CVRAM_108_recon CVRAM_109_recon CVRAM_111_recon CVRAM_112_recon CVRAM_113_recon CVRAM_114_recon CVRAM_115_recon CVRAM_117_recon CVRAM_118_recon CVRAM_119_recon CVRAM_120_recon CVRAM_121_recon CVRAM_122_recon CVRAM_124_recon CVRAM_125_recon CVRAM_126_recon CVRAM_127_recon CVRAM_128_recon CVRAM_129_recon CVRAM_130_recon CVRAM_131_recon CVRAM_132_recon CVRAM_133_recon CVRAM_135_recon CVRAM_136_recon CVRAM_138_recon CVRAM_139_recon CVRAM_140_recon CVRAM_142_recon CVRAM_143_recon CVRAM_144_recon CVRAM_145_recon CVRAM_146_recon CVRAM_147_recon CVRAM_148_recon CVRAM_149_recon CVRAM_151_recon CVRAM_152_recon CVRAM_153_recon CVRAM_154_recon CVRAM_155_recon CVRAM_156_recon CVRAM_157_recon CVRAM_158_recon CVRAM_159_recon --no-segno 77 78 79 80 81 82 --subdir stats/wmparc-nonzero.stats --tablefile STATS2/stats_tables-cvram/WMparc_stats_nonzero_04082009.txt Building the table.. SUBJECTS_DIR : /autofs/space/lang_012/users/CVRAM ERROR: cannot find /autofs/space/lang_012/users/CVRAM/CVRAM_001_recon/stats/wmparc-nonzero.stats/aseg.stats Use --skip flag if you want to continue in such cases So, it seems that it recognizes the --subdir flag, but is still looking for aseg.stats instead of a specified statsfile. Does anyone have any suggestions? Thanks! Tori

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Freesurfer April 2009