Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

FreeSurfer 6.0.0 CentOS 7 compatibility
by Vanzo, Davide 25 Sep '18

25 Sep '18

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if the current stable release works correctly on CentOS 7 or not? Thank you. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu

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longitudinal hippocampal aseg editing
by Rebecca Ray 25 Sep '18

25 Sep '18

External Email - Use Caution Martin, That is the point. I have edited the hippocampus in the -long 2 times and the recon does not maintain my edits. I would love any help to changes I should be making to my recon statement to maintain my edits. Rebecca Hi Rebecca, aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits ) Best, Martin On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote: >* External Email - Use Caution *>* HELP *>* ---------- Forwarded message ---------- *>* From: Rebecca Ray <rayr5 at gene.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Date: Thu, Sep 6, 2018 at 12:05 PM *>* Subject: longitudinal hippocampal aseg editing *>* To: freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *> > >* I have 2 time points on 60 subjects with most being in some form of *>* AD. There are considerable differences in hippocampal volume between *>* time points. I edited the raw images before making the template. I *>* then had to edit the aseg template image and there were still *>* problems on the -long images. I tried to edit and rerun autorecon2- *>* noaseg and autorecon3 and it does not appear to be keeping my edits. *> >* What am I doing wrong? *> >* Rebecca *> >* _______________*

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Research Assistant Job, Chicago, IL
by Jaiashre Sridhar 25 Sep '18

25 Sep '18

External Email - Use Caution Research Assistant job available at Northwestern University’s Mesulam Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. Job Summary: This position is within Dr. Emily Rogalski’s laboratory, which focuses on aging and dementia research including Alzheimer’s, primary progressive aphasia, frontotemporal dementia and SuperAging. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathological aging. Duties include coordinating PET and MRI scans, and analyzing the resultant structural and functional imaging data. The candidate will also be administering and scoring neuropsychological tests. Additional duties include working on graphics for manuscripts and grants or other general lab responsibilities. Minimum qualifications: - The candidate must hold a Bachelor’s degree - Familiarity with scripting in Python/Bash/MATLAB/R - A two-year commitment is requested Preferred qualifications: - Relevant backgrounds would be in Neuroscience, Biology, Psychology, and Biomedical Engineering - Experience using Freesurfer or other neuroimaging platforms - Experience administering and scoring neuropsychological tests Interested candidates, please email your CV to jaiashre.sridhar(a)northwestern.edu<mailto:jaiashre.sridhar@northwestern.edu>. A job posting will be available soon at careers.northwestern.edu<http://careers.northwestern.edu/>. --- Jaiashre Sridhar, MS Research Project Coordinator Northwestern University | Mesulam Cognitive Neurology and Alzheimer’s Disease Center 320 E. Superior St. | Searle 11-579 | Chicago IL 60611 Phone: (312) 503-1749 | Email: jaiashre.sridhar(a)northwestern.edu<mailto:jaiashre.sridhar@northwestern.edu> Web: www.brain.northwestern.edu<http://www.brain.northwestern.edu>

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error with trac-all -prep
by Vinny K 25 Sep '18

25 Sep '18

External Email - Use Caution Hi, I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4. I get the following error when running the command: trac-all -prep -c dmrirc. Any help would be greatly appreciated. Thanks, Vinny /home/Vinit/freesurfer/subjects/diffusion/Subj1 flirt.fsl -ref /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii -in /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0 Wed Sep 19 20:29:11 DST 2018 /home/Vinit/freesurfer/subjects/diffusion/Subj1 flirt.fsl -ref /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii -in /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat -init /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30 17:31:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018

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Misregistration of T2 FLAIR during recon-all
by Albrecht, Daniel S. 24 Sep '18

24 Sep '18

Hello, I’m trying to update recon-all (with freesurfer-6) on a number of subjects using T2 FLAIR images and the following command: recon-all -subjid <subject_name> -FLAIR <path_to_FLAIR.nii.gz> -FLAIRpial -autorecon3 For a substantial portion of subjects, the registration of the FLAIR image to the T1 fails. I’ve run a few trials where I pre-registered the FLAIR to the T1 and made sure the header information was the same (with fslcpgeom), but the registration during recon-all still fails (see images below). I saw a few posts from a couple years back about a recon-all patch that may fix the registration issue: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39378.html Is this the best way to deal with this issue? Thanks very much, Dan [cid:image001.jpg@01D45260.EDE8C4E0]

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Missing files in mri_glm
by srishti goel 24 Sep '18

24 Sep '18

External Email - Use Caution Hi, I am running analysis to compare group difference in thickness between two groups. I followed all the steps outlined on the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. Everything seemed to work fine except I didn't get the following files in each contrast's directory efficiency.dat pcc.mgh z.mgh I don't understand why those files don't show up as I didn't get any errors. Any help is appreciated. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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Available postdoctoral position in Norway: application deadline September 30th
by Alexander Olsen 24 Sep '18

24 Sep '18

External Email - Use Caution There is a temporary position available at the Department of Psychology as postdoctoral fellow in multimodal neuroimaging for a period of 2 years.The postdoctoral fellow will work at the Clinical Neuroscience Laboratory (CNL)<http://www.ntnu.no/web/psykologi/cnl>, headed by Associate professor Alexander Olsen. The successful candidate will develop work that contributes to, and complements, ongoing research studies. The postdoctoral fellow will have a key role in our research activities linked to the ENIGMA Brain Injury<http://enigma.ini.usc.edu/ongoing/enigma-tbi/> working group. ENIGMA is a framework with harmonized protocols for data processing and analysis across multiple sites and cohorts. The postdoctoral fellow will work in close collaboration with our world-wide partners to provide new knowledge on the consequences of traumatic brain injury by utilizing an unprecedented sample size compared to typical neuroimaging studies. Salary starting at 515 200 NOK ($ 62 000) per year. Read more about the position, and how to apply: https://www.jobbnorge.no/ledige-stillinger/stilling/149964/postdoctoral-pos… Feel free to contact me for any questions. Sincerely, Alexander Olsen Associate Professor Clinical Neuropsychologist Norwegian University of Science and Technology St. Olavs Hospital Trondheim, Norway Telephone: +47 917 22 824 http://www.ntnu.edu/employees/alexander.olsen

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Re: [Freesurfer] make_average_subject error
by C.P.E. Rollins 24 Sep '18

24 Sep '18

External Email - Use Caution Hi Douglas, Yes - attached here is the make_average_subject.log file. The command used was: make_average_subject --out average_v2 --subjects $(cat subjects.txt) subjects.txt also attached. Thanks again for your help Colleen

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PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen
by Caspar M. Schwiedrzik 24 Sep '18

24 Sep '18

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European Neuroscience Institute (ENI-G) and the German Primate Center <http://www.dpz.eu/de/startseite.html> (DPZ) in Göttingen, Germany is looking for an outstanding PhD student interested in studying the neural basis of perceptual learning in vision. The project investigates neural mechanisms of learning and perception at the level of circuits and single cells, utilizing functional magnetic resonance imaging (fMRI) in combination with electrophysiology and behavioral testing in humans and non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL; “Specificity or generalization? Neural mechanisms for perceptual learning with variability”). The PhD student’s project will focus on developing new perceptual learning paradigms and investigating the neural basis of perceptual learning in humans using fMRI. In addition, the PhD student will cooperate with other lab members on parallel electrophysiological and fMRI experiments as well as comparative research exploring the same questions in non-human primates. The lab seeks to understand the cortical basis and computational principles of perception and experience-dependent plasticity in the macaque and human brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition) To this end, we use a multimodal approach including fMRI-guided electrophysiological recordings in non-human primates and fMRI and ECoG in humans. The PhD student will play a key role in our research efforts in this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ ( http://www.dpz.eu) which are interdisciplinary research centers with international faculty and students pursuing cutting-edge research in neuroscience. The PhD student will have access to a new imaging center <http://www.dpz.eu/en/infocenter/> with a dedicated 3T research scanner, electrophysiology, and behavioral setups. ENI-G is engaged in experimental molecular and cellular research on the central and peripheral nervous systems as well as cognitive and systems neurosciences research. ENI is part of the University Medical Center Göttingen and associated with the Max Planck Society. The University Medical Center Göttingen is a tertiary care center. Its 7,400 employees work in over 65 departments and facilities to provide top-quality patient care, excellent research and modern teaching facilities. Göttingen provides a vibrant and stimulating neuroscience community with a strong background in computational as well as experimental neurosciences. The PhD student will have the opportunity to join one of the fourteen programs of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (http://www.ggnb.uni-goettingen.de) Your profile: The position will be available starting in November 2018 with an initial appointment for 3 years and a salary according to 50% TVL-13. Candidates should have a degree (master, diploma or equivalent) in a relevant field (e.g., neuroscience, psychology, biology), and ideally prior experience in fMRI, strong quantitative, programming, and experimental skills, and share a passion for understanding the neural basis of visual perception and its plasticity. Interested candidates should send their curriculum vitae, a description of their scientific interest and the names and contact information of up to two references who are able to comment on your academic background and who agreed to be contacted to c.schwiedrzik(a)eni-g.de, preferably before October 10th, 2018, but later expressions of interest will be considered until the position is filled. A good command of English is a requirement, but fluency in German is not essential. Please apply by 10.10.2018 to: Universitätsmedizin Göttingen European Neuroscience Institute Göttingen Neural Circuits and Cognition Lab Dr. Caspar Schwiedrzik Grisebachstr. 5 37077 Göttingen Germany Tel.: +49-(0)551-39-61371 E-Mail: c.schwiedrzik(a)eni-g.de

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Re: [Freesurfer] mri_glmfit-sim error
by C.P.E. Rollins 24 Sep '18

24 Sep '18

External Email - Use Caution Hi Douglas, Yes, the file (/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white) exists, I can view it in Freeview and have read permissions. I had recently tried downloading this patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ as I was equally having issues with make_average_subject and had found this forum post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57023.html Not sure if the problem might then be with mri_surfcluster.bin ? Thanks again, Colleen

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Freesurfer September 2018