Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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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Visualization fo brain vessels
by Patrik Krumpolec 24 Sep '18

24 Sep '18

External Email - Use Caution Good morning! I want to ask if it is possible to visualize compartment of brain vessels in freesurfer through freeview. Thank You very much and have a nice day! patrik krumpolec

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calculated cortical thickness from segmented binary gray matter and white matter images from other software
by yuanchao.zhang8＠gmail.com 23 Sep '18

23 Sep '18

External Email - Use Caution Dear experts, Is there any way I can calculate the cortical thickness based on gray matter and white matter binary images from other software. I mean I have a image in native space with white matter voxels labelled as 10 and gray matter voxels labelled as 5. Is there any way I can manage to calculate the cortical maps from this image using freesurfer? Thanks a lot! Best, Yuanchao Zhang yuanchao.zhang8(a)gmail.com

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make_average_subject error
by C.P.E. Rollins 23 Sep '18

23 Sep '18

External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but am receiving the following error: Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault (core dumped) Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 2018 I've attached here the full log file. I read in this forum: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html to try installing the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ and had asked our computing support team to install it before the current run of make_average_subject, so the error seems to be happening despite the patch. I would greatly appreciate your suggestions for resolving the error. Thanks very much, Colleen

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