Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

error in manual edit by freeview
by 陈聪 17 Aug '16

17 Aug '16

Hi dear all I am using freeview to edit segmentation, I found one slice in coronal view in brainmask.mgz mismatch with other slice, this slice obviously move down. WM and T1.mgz are normal, I don’t know how to move this wrong slice back. Any advice will be appreciated. thanks very much. CONG

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recon-all version update not showing in log file
by Donna Cosgrove 17 Aug '16

17 Aug '16

Hi, I am updating previously recon'd datasets done with FS versions 4.4 and 5.2 to v5.3. I'm running the recon-all command on the previously done subjects to retain any edits. However, when I had a look at the recon-all.log, it still has a date from the previous recon in 2013. The pctsurfcon.log contains this info (below) with an updated date, but nothing else seems to have updated... -------------- Logfile for pctsurfcon Sun Aug 14 06:12:59 IST 2016 setenv SUBJECTS_DIR /home/psych_lab/Desktop/freesurfer/FREESURFER_ DONE cd /home/psych_lab/Desktop/freesurfer/FREESURFER_D ONE /CON9231/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux nuig-79JP212-Ubuntu 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer Cleaning up ------------- T he command I'm using recon-all -all -s SUBJ_ID seems to works fine, even identifying initially in the terminal that the build stamps do not match. It does also take much less time than a recon from scratch. Any thoughts would be appreciated. Thanks for your help! Donna

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ISMRM diffusion workshop: -1 month!
by Tim Dyrby 17 Aug '16

17 Aug '16

Dear FreeSurfers, This is just a reminder that the countdown for the ISMRM workshop on breaking the barriers of diffusion MRI has started. The meeting will take place in Lisbon, 11-16 September. Please check http://www.ismrm.org/workshops/Diffusion16/ <http://www.ismrm.org/workshops/Diffusion16/> for program and updates. The registration is still open! However, please note that accommodation at the Sheraton Lisboa hotel is still available *but not at the discounted ISMRM rate* (all the rooms have gone!). Alternative options can be found at http://www.ismrm.org/workshops/Diffusion16/housing.htm. <http://www.ismrm.org/workshops/Diffusion16/housing.htm.> Looking forward seeing you there. Best, Tim -- Tim B. Dyrby Associate Professor Danish Research Centre for Magnetic Resonance (DRCMR), section 714 Center for Functional and Diagnostic Imaging and Research Copenhagen University Hospital Hvidovre Kettegård Allé 30 2650 Hvidovre Denmark Office phone: +45 38626542 Mobile:+45 40790282 web: http://dig.drcmr.dk and www.drcmr.dk & Image Analysis and Computer Graphics section Department of Applied Mathematics and Computer Science Technical University of Denmark Richard Petersens Plads, Building 324 2800 Kongens Lyngby Denmark Office Phone: +45 45253424

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Subject: Re: Zero cortical thickness
by A Nunes 16 Aug '16

16 Aug '16

Hi Douglas, I meant a surface area extracted from a surface based atlas. Thanks Adonay

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pial_lgi table
by Chatzi, Vasiliki 16 Aug '16

16 Aug '16

Dear developers, I was wondering if you could let me know how can I extract a table for the measure pial_lgi. Best wishes, Vasiliki Vasiliki Chatzi, BA(Hons) MSc PhD student | Department of Psychosis studies Institute of Psychiatry, Psychology and Neuroscience | King's College London

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recon-all -base -all, "Word too long" error.
by Hanbyul Cho 16 Aug '16

16 Aug '16

Dear FreeSurfer experts, I am FreeSurfer longitudinal processing the thirty time points data. When I tried the step 2 process to make a template, the process stopped with an error. The error message as the below. =============== ... mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.mgz /home/Desktop/MyProject/CO30/mri/rawavg.mgz Volumes differ in geometry row=1 col=1 diff=0.054242 (0.054242) ************************************************************ ******************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ************************************************************ ******************* Word too long. ================== My command line was: recon-all -base SET1template -tp CO01 -tp CO02 ... -tp CO30 -all How can I fix the error? Best wishes, Han

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Iglesias paper: Hippocampal subfields
by Jacobs H (NP) 15 Aug '16

15 Aug '16

Hi! I would like to create a 3D rendering of the hippocampal subfields generated by FreeSurfer (as done in the Iglesias paper). I have tried to do this using Slicer, but the results are not that nice (making a model based on the 1mm mgz file). How were the surfaces in the paper generated? Do you have any suggestions for me on how to do this? Many thanks Heidi

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Zero cortical thickness
by A Nunes 15 Aug '16

15 Aug '16

Hi, I have read in the mailing list about zero cortical thickness, but I still have some doubts. I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all subjects is zero, I would guess is not considered cortical, however, all my areas are cortical. - If I compute a ttest against two groups, should I set the zeros as NaNs? or are the zero thickness meaningful (a genuine measure or a segmentation artifact)? -Should I use the -l ?h.cortex.label to avoid having zero thickness in some areas? If so, at which point? the commands used are: mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h --sval-annot fsaverage/label/?h.areas.annot --tval $SUBJECTS_DIR/subjid/label/?h.areas.annot mris_anatomical_stats -a $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b subjid ?h Thanks Adonay

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Job postings: Post-doc & Data manager/programmer
by Gregory Book 15 Aug '16

15 Aug '16

The Olin Neuropsychiatry Research Center, located in Hartford CT, USA is looking to fill 2 open positions. The Olin Neuropsychiatry Research Center has an opening for a post-doc specializing in neuroinformatics, big-data analysis, and machine learning. The Olin Center is the psychiatric research center within Hartford Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an internal historical database of nearly 13,000 MRI sessions, and a 400-core Linux compute cluster. The candidate will pursue their own research with a focus on neuroinformatics and big-data analysis and assist multiple principle investigators with large scale analyses. The candidate will contribute to the development of the open-source Neuroinformatics Database ( http://github.com/gbook/nidb) and publish journal articles on their own research and software development. MS degree in engineering, science, neuroscience, or psychology is required, PhD preferred. Candidate is expected to have experience in SQL programming and at least one other programming language. Proficiency in multiple programming languages such as Perl, C, C++, JavaScript, PHP, Matlab, and Python is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org 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. Proficiency in multiple programming languages is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org

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dividing Freesufer subfields into one anterior, middle and posterior region
by Erik Lindberg 15 Aug '16

15 Aug '16

Dear FS experts. I want to divid the FS subfield segementation into a anterior part, one middle part and posterior segment - or potentially divide the rang into 10% of the whole rang - and then move backword until I extracted 10 subparts. Is there some way I can do that? Thanks Erik

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