Freesurfer

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30088 discussions

Error when execute preproc-sess
by raul perez moraga 26 Sep '18

26 Sep '18

External Email - Use Caution Hello Freesurfer community I am trying to do a fMRI analysis and I am following the tutorial of FSFAST, but when I try to execute preproc-sess command I get a error if: Expression Syntax I used this command: preproc-sess -s resting -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Also I attach the output log. My Freesurfer version is 6.0.0 My OS CentOS Linux release 7.4.1708 (Core) Thank you. Raul

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Vertex position
by Karin Westin 26 Sep '18

26 Sep '18

External Email - Use Caution Hi! Is it possible to retrieve a map or table indicating exactly where on the cortex a vertex with a specific id number is located? Best and thanks, Karin

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Hippocampal-Amygdala subfields error
by Miguel Ángel Rivas Fernández 25 Sep '18

25 Sep '18

External Email - Use Caution Hello Freesurfer devs, I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects: *Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)* *MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 2018, 21:37:33 CEST* What would be the reason? Thanks in advance, Best wishes, -- *Miguel Ángel Rivas Fernández*

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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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