Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

fsaverage error with recon-all
by chen 16 Jun '19

16 Jun '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set, but batching exited with an error. According to recon-all.log, there is no such a file or directory (INFO:trgsubject = srcsubject). It could not read fsaverage/surf/lh.white. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. The detail information please see the attachments.Thanks in advance.Jiachen ------------------

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Postdoc position opening at Brown University in cognitive aging and Alzheimer’s disease
by Hwamee Oh 16 Jun '19

16 Jun '19

External Email - Use Caution We are seeking a highly motivated postdoctoral researcher to study behavioral and neuroimaging markers of preclinical Alzheimer’s disease in the Warren Alpert Medical School of Brown University. The primary performance site for this postdoctoral fellowship is in the Butler Hospital Memory and Aging Program (MAP). Brown University has a strong commitment to brain science and research in neurodegenerative disorders. This commitment is united under The Carney Institute for Brain Science and the new Center for Translational Neuroscience (CTN). The mission of the Carney Institute and CTN is to promote the discovery and innovation in brain science by supporting a diverse community of experimentalists, theorists, engineers, and clinicians. The MAP, one of the leading clinical trial centers for Alzheimer’s disease (AD) in the United States, is committed to accelerating drug and biomarker development for AD and to training young investigators for careers in AD research. The successful candidate will join a team of experts in Aging, Alzheimer’s disease, and related dementia research. This postdoctoral position is primarily focused on the area of the cognitive system in aging and preclinical Alzheimer’s disease and will work on developing early behavioral and neuroimaging markers of Alzheimer’s disease and integrating structural and functional MRI, PET, cognitive, genetic, and biofluid measures from ongoing or completed projects. Fellows will have ample opportunities to explore and gain experience with multidisciplinary and clinical research in aging and Alzheimer’s disease and to interact with core faculty members in the MAP and the Carney Institute of Brain Science at Brown University. Applicants with a Ph.D. degree in cognitive neuroscience, neuropsychology, biomedical engineering, electrical engineering, computer science, physics or a relevant field are encouraged to apply. Prior experience with human neuroimaging (e.g., task fMRI, rsfMRI, MRI, DTI, ERP, PET), a strong background in cognitive neuroscience and experimental design, and familiarity with programming in relevant languages (e.g., Python, MATLAB, C) are desirable. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive and brain aging, Alzheimer’s disease, and/or neuroimaging, and the ability to independently develop research questions and work in collaboration with other team members. The MAP is part of the Department of Psychiatry and Human Behavior at the Warren Alpert Medical School of Brown University, which is located in Providence, Rhode Island. Providence is within one hour from Boston and 3 hrs from New York City by train/subway and provides an intellectually and culturally rich environment with a reasonable living cost. Please note that this postdoctoral position is research-centered and prior clinical experience is not required. Pursuing licensure for a clinical neuropsychologist is optional. The postdoctoral position is supported by the fellowship program up to 2 years, with a possibility of support in year 3 depending on funding. The expected start date is late Summer 2019. Review of applications will begin immediately and continue until the position is filled. Interested persons can find more information on the position in the websites listed below. This postdoctoral fellowship is administered though the Research Fellowship Program within *The Alpert Medical School of Brown University, Clinical Psychology Training Programs at Brown: A Consortium of the Providence VA Medical Center, Lifespan, and Care New England. * The program’s website is located here: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… A full description of the fellowship position can be found in the link below under the section “Alzheimer’s Research – Neuroimaging” in “Neuropsychology Track” under “Research Fellowship Program (RFP): https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… Details regarding application, are located here under “Application Details”: https://www.brown.edu/academics/medical/about/departments/psychiatry-and-hu… NOTE: As explained on the application page of our website, applications are submitted through the APPA CAS portal. Instructions are located on the webpage. For more information about the research and the position, please contact Dr. Hwamee Oh, the Director of Imaging Research in the MAP, at hwameeoh(a)gmail.com.

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How do I get FreeSurfer to use a custom Talairach target.
by Aaron Tanenbaum 16 Jun '19

16 Jun '19

External Email - Use Caution I am wondering if there is any documentation about getting FreeSurfer to use a custom Talairach target.

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Yeo Atlas Download
by Aster, Hans-Christoph 15 Jun '19

15 Jun '19

External Email - Use Caution Dear Freesurfer Team, I cannot download the "Resting State Cortical Parcellation in nonlin MNI152 space" with several machines. Is there something wrong with the server? The error message is: Server Connection was reset. Thank you in advance, kind regards Hans --- Dr. med. univ. Hans-Christoph Aster Neurologische Klinik Universitätsklinikum Würzburg Josef-Schneider-Str. 11 D-97080 Würzburg Tel. +49 931 201 23668 Aster_H(a)ukw.de<mailto:Aster_H@ukw.de> http://www.neurologie.ukw.de/

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fsaverage error with recon-all
by chen 14 Jun '19

14 Jun '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Batching exited with an error indicating there is not fsaverage/surf/lh.sphere.reg. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. The detail information please see the attachments.Thanks in advance.Jiachen ------------------

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incompatible vertex number ???
by Barletta, Valeria 14 Jun '19

14 Jun '19

Dear Freesurfers, I am getting this type of error in the Terminal when I open my images on Freesurfer: MRISreadNewCurvature: incompatible vertex number in file /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv No such file or directory could not read curvature from curv No such file or directory mpatible vertex number in file /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv I can still visualize and modify the images, but I noticed that recon-all autorecon2-wm for wm edits is not working. Are these two things related? Thank you, Vale

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Cannot convert mgz to nii
by Ritesh Mahajan 14 Jun '19

14 Jun '19

External Email - Use Caution Hello Team, I was working on mind boggle data set. I downloaded the freesurfer results from "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/HM…" I am unable to convert aseg.mgz to aseg.nii for HLN group. Please note that i was able to convert all other groups(MMRR, NKI-TRT, NKI-RS). Command i tried "mri_convert aseg.mgz to aseg.nii" it throws cannot allocate memory error, where as it works for all other series other than HLN. I have attached the screen shot of error message for your reference. Can you please help me out? Thanks, RItesh Mahajan

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Recon-all taking 20 hours to run.
by Aaron Tanenbaum 13 Jun '19

13 Jun '19

External Email - Use Caution I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. The super computer is about 3 years old. Of those 38 subjects, 7 exceeded 20 hour time limit on the batch script. The others took about 12 hours to finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the command I used for one of them. Is there a reason for some subjects recon-all would take more then 20 hours? recon-all -s 100000016_20170414 -i /scratch/brierm/Images/100000016_20170414_T1.nii -FLAIR /scratch/brierm/Images/100000016_20170414_FLAIR.nii -FLAIRpial -all -mprage -hippocampal-subfields-T1 -qcache

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Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception
by fsbuild 12 Jun '19

12 Jun '19

External Email - Use Caution Hello Wafaa, I believe qdec runs as a 32 bit application.  You may see Mac OS 10.14 put up a window warning that an application is not optimized for the system and needs to be re-compiled by its developer; that means it is a 32 bit app.  While many 32 bit apps that ran on High Sierra (10.13) run on Mojave (10.14), I don't think it is guaranteed they will run OK on 10.14, e.g., qdec trying to use 32 bit floats while Mac OS 10.14 is expecting apps to use 64 bit floats.  I do know that 32 bit apps will not run at all on the next rev of Mac OS that was just announced, Catalina, Mac OS 10.15.  I don't know if there is a 64 bit version of qdec. - R. Wafaa Sweidan June 12, 2019 at 12:54         External Email - Use Caution         Hello all, I have been using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on macos high sierra, then I updated to mojave 10.14. freeusrfer was working all good for a while. BUT, for unknown reasons, I am no longer able to overlay the significance maps using tksurfer and cant open qdec, like below: command: tksurfer fsaverage lh inflated output error: subject is fsaverage hemi    is lh surface is inflated surfer: current subjects dir: /Users/wsweidan/Desktop/GLM_trial surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer:     /Users/wsweidan/Desktop/GLM_trial checking for nofix files in 'inflated' Reading image info (/Users/wsweidan/Desktop/GLM_trial/fsaverage) Reading /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: Reading header info from /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Error sourcing /Applications/freesurfer/tktools/tksurfer.tcl: bad distance "0.125i": can't be negative reading white matter vertex locations.... % Floating exception command: qdec output error: Floating exception I reinstalled freesurfer again and I still get the same errors. Freeview works just fine. Any input of how to solve this issue?  Thanks in advance,  Wafaa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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multi-slice timing correction
by Joseph Dien 12 Jun '19

12 Jun '19

External Email - Use Caution Hi Doug, I’m happy to see that FreeSurfer6 provides enhanced support for slice timing. I’m trying to run it on some multi-slice data. May I ask you for some guidance on how to use the new preproc-sess options? As I understand it, I would specify “-ngroups 10” because the data were collected in ten groups of six slices at a time? I’m not sure how to specify “-sliceorder”. Slice times are below. Thanks for any help you can provide. Joe 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 0 877.500000000000 502.500000000000 125 1005 627.500000000000 252.500000000000 1130 752.500000000000 377.500000000000 -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com

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Freesurfer June 2019