Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

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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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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Postdoctoral research fellows, University of Oslo, Norway
by Lars Tjelta Westlye 05 Apr '16

05 Apr '16

2 three-year positions as Postdoctoral Research Fellow at the Norwegian Centre for Mental Disorders Research, University of Oslo are currently available. http://uio.easycruit.com/vacancy/1599437/65775?iso=no NORMENT is a Norwegian Centre of Excellence, and coordinates a translational multicenter study involving all University hospitals in Oslo and several groups at the Universities of Oslo and Bergen. The main aims are to disentangle the mechanisms of severe mental illness. NORMENT Multimodal Imaging group includes eight postdoctoral fellows and several PhD and graduate students, and is directly involved in various international collaborations. * Job description The postdoctoral fellows will play a central role in the analysis and dissemination of a large imaging genetics database, in particular focusing on methods for integrating multimodal imaging (sMRI, ASL, DTI, fMRI) and genetic data. * Qualifications The ideal candidate is ambitious and highly motivated for pursuing a career in science, hold a PhD in psychology, neuroimaging, computational or cognitive neuroscience, biomedical engineering, biostatistics, or equivalent, have a strong background and interest in neuroscience, genetics, and an excellent publication record. Experience with MRI analysis tools including Freesurfer and FSL, and expertise in brain network and connectivity analysis, or multivariate pattern recognition or machine learning techniques is an advantage. * Applying for the positions The application is to be submitted electronically and must include application letter, CV, copies of educational certificates and letters of recommendation, list of publications, up to five published papers that the applicant wishes to be considered by the evaluation committee, references. Yearly salary: NOK 483 700-560 700, depending on qualifications and experience. Application deadline: April 21 2016. For any informal enquiries, please contact Lars T. Westlye (l.t.westlye(a)psykologi.uio.no) http://uio.easycruit.com/vacancy/1599437/65775?iso=no? ---- Lars T. Westlye, PhD Senior Researcher, Head of Multimodal Imaging Group NORMENT CoE, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway Associate Professor II, Department of Psychology, University of Oslo Email: l.t.westlye(a)psykologi.uio.no | Phone: +47 971 63 221

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Structural resolution and longitudinal processing
by Angstadt, Mike 04 Apr '16

04 Apr '16

We have a large number of scans that have been processed through the standard cross-sectional stream. Subjects have a number of repeated scans, so we now want to take advantage of the longitudinal stream. When first beginning to run subjects through longitudinal template creation, we noticed a warning message in some cases in the log: ******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ******************************************************************************* Looking into it, there does indeed appear to have been a change in the reconstruction stream that led to images at different times during the study to have slightly different voxel dimensions, changing from 1x1x1.2 to 1.01x1.01x1.2mm voxels. Our question is if there is some way to fix this prior to starting the longitudinal stream but without having to redo the original cross-sectional processing and editing that has been completed? -- Mike Angstadt Research Computer Specialist / PANLab Lab Manager Department of Psychiatry / University of Michigan (734) 936-8229 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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white matter parcellation
by Holleran, Laurena 04 Apr '16

04 Apr '16

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PostDoc Position - Deep Learning in Neuroimaging of AD - Barcelona
by Juan Domingo Gispert López 04 Apr '16

04 Apr '16

The Barcelonaβeta Brain Research Centre (BBRC) welcomes applications for a full-time research position to develop deep learning methods to predict the onset of Alzheimer’s disease and its preclinical stage based on neuroimaging and other wet biomarkers, as part of its clinical research program. The full job description can be found here: https://fpmaragall.org/en/wp-content/uploads/sites/3/2014/07/BBRC_Researche… Qualifications: - PhD in Neuroscience, Medicine, Computer Science, Bioengineering or related disciplines (It is mandatory for the candidates to hold a PhD) - Proven experience in modelling and/or deep learning is required. - Strong understanding of the biological basis of AD and the course of AD biomarkers is needed. - Experience in neuroimaging and/or genetic data analysis would be positively considered. - Proven record of first authorship and co-authorship on scientific is required. Skills: - Experience working with large and multidisciplinary data sets is required. - Database manipulation skills, with strong attention to detail. - Proven ability to lead and orientate a team of computer scientists - Interest in joining a non-profit organization with a mission of high social impact. - Strong interpersonal skills (empathic and focused team-worker). - Ability to think independently and work collaboratively. Benefits: - Starting date: Second quarter 2016. - The research position is scheduled initially for two years (open to renewal). - Salary will depend on experience. In order to apply: Please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: cminguillon(a)fpmaragall.org Deadline for submitting applications: April 29th 2016. -- Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. *This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation.*

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Freesurfer dev error
by Nathan Malitz 01 Apr '16

01 Apr '16

recently download and trying the dev version of freesurfer 6. it exited with this error #@# Cortical Parc 2 lh Fri Apr 1 13:41:04 AEDT 2016 /usr/local/freesurfer6/subjects/test/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 testphp lh ../surf/lh.sphere.reg /usr/local/freesurfer6/average */lh.CDatlas.2016-03-20* ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ GCSAread(/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20): could not open file reading atlas from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20... No such file or directory mris_ca_label: could not read classifier from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20 No such file or directory recon-all -s test exited with ERRORS at Fri Apr 1 13:41:08 AEDT 2016 This file doesn't exist in the directory, neither does the rh one, is it called something else or missing from the build? I'd prefer not to download 9GB again, is it available by itself? any ideas? -- *Nathan Malitz* <http://www.miconsult.com.au/>

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Labeled Nifti atlases
by Gregory Book 01 Apr '16

01 Apr '16

Are there any labeled nifti atlases that correspond to the freesurfer parcellation atlases output from recon-all? I'm basically interested in visualization of group results. -Greg

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Mismatch in dimensions using mri_label2vol
by Afzal, Afsana 01 Apr '16

01 Apr '16

Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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