Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Nonisotropic PSF in mri_gtmpvc
by Ian Kennedy 06 Apr '16

06 Apr '16

Hello, Is there a way to specify a nonisotropic PSF when using mri_gtmpvc? I have reason to believe there are differences between the axial and transverse resolutions of the PET scanner in my study and would like to incorporate them if possible. Thanks, Ian Kennedy

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Data manager/programmer position
by Gregory Book 06 Apr '16

06 Apr '16

The Olin Neuropsychiatry Research Center is seeking a data manager/programmer to help maintain neuroimaging databases in support of multiple NIH funded projects. The Olin Center is a neuropsychiatric research center within Hartford Hospital’s Institute of Living campus. We house a 3T MRI, multiple EEG, TMS, and eye tracking systems, an internal database of nearly 13,000 MRI sessions, and a 400-core compute cluster. The primary responsibilities of the data manager will be to maintain internal and public imaging databases by performing the following tasks: remove personally identifiable information, perform uploads to NIH repositories, identify missing data, organize identifiers, support remote sites with data importing/uploading, and ensure data redundancy and backups. Additionally, the data manager may contribute to the development of the Neuroinformatics Database (http://github.com/gbook/nidb) using SQL, PHP, Perl, C++ and other programming languages for the purpose of making data management more efficient and robust. The data manager also will have the opportunity to participate in research projects and contribute to manuscripts. Bachelor’s degree in engineering, science, neuroscience, or psychology is required, Masters or higher is preferred. Candidate is expected to have experience in SQL programming and at least one programming language. Proficiency in multiple programming languages is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org

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octave permission denied
by stdp82＠virgilio.it 06 Apr '16

06 Apr '16

Hi list,this error occurs using octave in FS-FAST.Thanks, Stefano ------- octave output -------------------- LD_LIBRARY_PATH :/usr/local/octave/3.8.0/lib /usr/local/octave/3.8.0/bin: Permission denied. ------------------------------------------ ERROR: fast_selxavg3() failed\n

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segmentation fault mri_convert Ubuntu 14.04 again
by Griffa Alessandra 06 Apr '16

06 Apr '16

Dear all, I get a segmentation fault when running mri_convert, FreeSurfer version 5.0.0 on a fresh Ubuntu 14.04 installation. In the past, and on a different machine, I could fix this problem by copying the Ubuntu_12.04 file libcrypt-2.*.so to the $FREESURFER_HOME/lib folder of the Ubuntu_14.04 machine (as suggested here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04052…) Anyway, on my new Ubuntu_14.04 machine, this trick does not work anymore and I cannot run FreeSurfer 5.0.0. Can somebody help me please? Thank you very much! Regards, Alessandra Griffa

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longitudinal pipeline surface error
by Mihaela Stefan 06 Apr '16

06 Apr '16

Dear FreeSurfers, We are doing a longitudinal analysis with three time points (MRI1, MRI2, MRI3). All the subjects were processed well except for one. The MRI3.long of that subject has very bad surfaces (see attachment - I am also attaching the log file). The cross, the template and the first two long runs were reconned well, though. We can't figure out why this third run is so bad. As a note, we processed all the cross runs on an Ubuntu machine but we ran the longitudinal pipeline on a computer cluster (both with freesurfer v5.3). We ran the long twice for that subject thinking that the pipeline crashed somehow the first time. However, the results were the same. Any help would be appreciated. Thanks! Mihaela

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dt_recon image inputs -i flag
by Chiu, Bryan (PHTH) 05 Apr '16

05 Apr '16

Hi, I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec and *nii.gz files that come out. In the tutorial it mentions the -i flag requiring a dcm image. Is it possible to pass a *.nii.gz file ? Regards, _______________________________________ Bryan Chiu Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia

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Installation issue
by stdp82＠virgilio.it 05 Apr '16

05 Apr '16

Hi list, I'm reinstalling FS on my PC (iMac end of 2012).This error occur: freeview /Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file not executable. Please take in account:freesurfer & [1] 1818 [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at: https://surfer.nmr.mgh.harvard.edu Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text. Direct comments and questions to: freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thanks Stefano

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White matter parcellation based on ROIs from fMRI
by Beyh, Ahmad 05 Apr '16

05 Apr '16

Hello Freesurfers, I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s. I want to use the ROIs for tractography, and therefore need them to include the underlying white matter. I I am aware that freesurfer can do this after running the subjects through recon-all using freesurfer's own atlas. But is there a way to do this using the cortical ROIs defined in native space? So can I give freesurfer the T1 and the cortical ROIs as input and get the volumetric ROIs (that include white matter) as output in each subject's native space? This is important because the ROIs come from fMRI and are not based on the anatomy. A detailed answer would be highly appreciated. Many thanks, Ahmad

1 0

License invalid for Development Version
by Jeurissen Ben 05 Apr '16

05 Apr '16

Dear Freesurfer experts, I am affected by the PERL incompatibility described in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043504.… . To get around this issue, I switched to the newest development version as suggested in that post. However, my license file (which worked fine with the stable version) is not recognised: "ERROR: Invalid FreeSurfer license key found in license file /home/ben/freesurfer/license.txt” Do I need a special license for the development version? How can I obtain it? Cheers, Ben - Ben Jeurissen, Ph.D. Post-doctoral researcher Vision Lab, Dept. of Physics University of Antwerp Universiteitsplein 1, N.1.18 B-2610 Wilrijk, Belgium Phone: +32 3 265 24 77 Email: ben.jeurissen(a)uantwerpen.be<mailto:ben.jeurissen@uantwerpen.be> Url: http://visielab.uantwerpen.be/people/ben-jeurissen<https://mail.uantwerpen.be/owa/redir.aspx?SURL=iz3BHzAIEzF8TwCIE-FGWB58qJgP…>

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Tracula problems (creating symbolic link)
by Efrat Kliper 05 Apr '16

05 Apr '16

Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 I encountered two problems: 1. When I run the initial code of Tracula: trac-all –prep code: /home/fsl/ usr/local/freesurfer/bin/trac-all -prep -c /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt Subject TB_480 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz ln: creating symbolic link `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not supported 2. If I run the trac-all –bedp command of Tracula (on already trac-all data which was preproc on Freesurfer version 5.1. /home/fsl /usr/local/freesurfer/bin/trac-all -bedp -c /home/fsl/Desktop/xxx.txt Subject TB_201 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /mnt/hgfs/linux_share/subjects/TB_201/dmri subjectdir is /mnt/hgfs/linux_share/subjects/TB_201/dmri /mnt/hgfs/linux_share/subjects/TB_201/dmri/data not found I am guessing those problems are from the same source. Do you have any suggestions on how can I resolve these issues? Is there a way to overcome the "ln" command and to create this data file without it? (I have also tried to run it from local OS linux and not from shared folder. Many thanks, Efrat

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