Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

octave fast_selxavg3() failed\n
by stdp82＠virgilio.it 06 Apr '16

06 Apr '16

Hi listthis 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

2 1

rcbf-merge
by Alshikho, Mohamad J. 06 Apr '16

06 Apr '16

Dear Experts, I am working on ASL analysis using Freesurfer's tools "rcbf-prep" and "rcbf-merge" I can't find the script "rcbf-merge" in Freesurfer 5.3 ( i.e when I call the command rcbf-merge in terminal, it returns as : command not found) Any suggestions are highly appreciated! Best, Mohamad

2 1

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

2 1

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

1 0

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

1 0

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

1 0

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

2 7

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

2 1

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

2 1

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

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Freesurfer April 2016