Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

ASEG Extraction Inquiry
by David S Lee 14 May '18

14 May '18

External Email - Use Caution Hi FreeSurfer Experts, I have extracted ASEG volumes using "asegstats2table" and have a few questions about the output. 1. I get values of "0" for Left and Right "WM-hypointensities" as well as "non-WM-hypointensities". Does the ASEG segmentation for WM-hypointensities only produce whole brain measures (Left and Right combined) ? 2. Most measures are separated by Left and Right, but some are not. So, are these values pertinent to both hemispheres (whole brain?) 3. Is there a reference page I can check to see what each of the measures mean (i.e. atlas)? Thank you for your time! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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differences between qdec display and summary file for monte carlo corrected results
by yuanchao.zhang8＠gmail.com 14 May '18

14 May '18

External Email - Use Caution Hi, freesurfer experts, As I mentioned in my last email, I see no answer. I think it is possible that my description is not clear enough. I used qdec to compare the cortical thickness of two groups and tried to correct for multiple comparisons using the button in qdec of monte carlo simulation. I saw only one big cluster in the display window of qdec, whereas I saw three clusters in the terminal (printed text in the terminal) and in the .summary file. What is the problem here? Why is there the difference between the two? Below are some contents of the mc-z.abs.th20.sig.cluster.summary file: # Input /fsdata/example/qdec/test2/lh-Diff-male-female-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /fsdata/example # SearchSpace_mm2 73217.3 # SearchSpace_vtx 141808 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.35442 at vertex 136194 # Overall min -8.31037 at vertex 29648 # NClusters 3 # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -8.310 29648 1472.33 -47.4 -7.6 44.8 0.00010 0.00000 0.00020 3372 -9795.07 precentral 2 -7.098 121377 277.37 -17.8 -15.5 63.6 0.02400 0.02200 0.02600 656 -1605.27 precentral 3 -4.500 83861 241.90 -36.3 51.7 -6.3 0.04790 0.04520 0.05060 326 -790.83 rostralmiddlefrontal In the qdec display window, I only saw the cluster 1, the other two clusters were not displayed. I also tried to visualize the result using freeview and loaded the mc-z.abs.th20.sig.vertex.mgh. I saw one cluster. but when I loaded the mc-z.abs.th20.sig.ocn.annot file, I saw three different clusters. Thanks a lot! Best, Yuanchao

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Postdoc position at Bangor University, UK
by Kami Koldewyn 14 May '18

14 May '18

External Email - Use Caution Applications are invited for a two year (with a possible 1-2 year extension), full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab<https://sites.google.com/view/devsocialvislab/> in the School of Psychology at Bangor University<https://www.bangor.ac.uk/psychology/> (Wales, UK). The post is part of a European Research Council funded Starting Grant focused on Developmental Social Neuroscience. The project, ‘Becoming Social’, investigates developmental change in social perception, social learning and the social brain in late-childhood/early adolescence. The successful applicant will be the coordinator of the longitudinal developmental aspects of the Becoming Social project, which focuses on the transitional period between childhood and adolescence. The post will involve developing tasks and methods that will be applied throughout the five-year project in the longitudinal developmental streams. Methods used may include behavioural, eye-tracking and neuroimaging (e.g. fMRI, DWI) measures and the postdoctoral researcher who fills this post will be very involved, both conceptually and technically, in the design and construction of research questions and the tasks to address them. Duties will include working to develop tasks and materials that will be used with both adults and children/adolescents aged 11-16 both with and without an Autism Spectrum Disorder. The postdoctoral researcher will be a key member of the Becoming Social team and will work closely with other team members. A PhD or equivalent in a relevant field (e.g., Psychology, Neuroscience, Cognitive Science, Biomedical Imaging/Engineering or Computer Science), as well as outstanding written and spoken communication skills are essential. In addition, experience working with children or adolescents and their families would be helpful for this post. Closing date for applications: 1st June, 2018. Exact timing of the start date is flexible for the right candidate. For full details, see this document: PDF of advertisement<applewebdata://31232B52-8FE5-41ED-91A3-7B5D0FC6327C/goo.gl/fuXtAM> To apply, visit: jobs.bangor.ac.uk — Job BU01592<https://goo.gl/3V4RMF> Please forward to anyone you think might be interested. And please contact me with any questions! -kami ________________________________ Kami Koldewyn, PhD Reader, School of Psychology Bangor University k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk> https://sites.google.com/view/devsocialvislab/ Mae croeso i chi gysylltu gyda'r Brifysgol yn Gymraeg neu Saesneg You are welcome to contact the University in Welsh or English Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Problems Extending the Pial Surface
by Saum Naderi 12 May '18

12 May '18

External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without affecting the wm boundary? Thanks, Saum

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correcting surface with optic chiam
by Alexopoulos, Dimitrios 11 May '18

11 May '18

External Email - Use Caution In many of our studies there appears to be a pial/wm surface associated with the optic chiasm. (See attached). Do these need to be corrected? If so, is it best to remove from the brainmask.mgz or from the wm.mgz? Jim "The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email." ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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how to reinsert volume geometry information into surf
by padma 11 May '18

11 May '18

Hi, I exported a freesurfer mesh to PLY format to do some computation and have exported the PLY surface back to an fsmesh. How do I put back the volume geometry information into the mesh surface? Thanks, —Padma

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run recon all with forced orientation, spacing and dimension
by Ritesh Mahajan 11 May '18

11 May '18

External Email - Use Caution Hello Team, As i know free-surfer generates the output with following: 1) Dimensions : 256*256*256 2) Spacing : 1, 1,1 mm 3) Orientation : LIA Is there any way to run free-surfer with user specified orientation, spacing and dimension ? Thanks, Ritesh Mahajan

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Re: [Freesurfer] V6 Stable OSX software error - multistrip flag - RESOLVED
by Matthew Grecsek 11 May '18

11 May '18

External Email - Use Caution Hi Andrew, I installed the development version and everything ran correctly to completion as you suggested. Thanks, -Matt On Mon, May 7, 2018 at 1:08 PM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Matt, this issue should be fixed in the freesurfer development version, > but as a temporary fix to get things working in v6, I would suggest > disabling SIP and rerunning: > > http://osxdaily.com/2015/10/05/disable-rootless-system- > integrity-protection-mac-os-x/ > > > > best > > Andrew > > > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Matthew > Grecsek <matt(a)grecsek.com> > *Reply-To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Thursday, May 3, 2018 at 1:31 PM > *To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] V6 Stable OSX software error - multistrip flag > > > > * External Email - Use Caution * > > I'm using the following flags on my recon -all: -mprage -time -multistrip > -subcortseg > > > and getting the following errors at this section of the log file: > > > > mri_watershed -rusage /Users/Matthew/Downloads/matt/ > mattmp/touch/rusage.mri_watershed.dat -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 5 T1.mgz > brainmask_T1_PFH5.auto.mgz \n > > \n mri_watershed -rusage /Users/Matthew/Downloads/matt/ > mattmp/touch/rusage.mri_watershed.dat -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 10 T1.mgz > brainmask_T1_PFH10.auto.mgz \n > > \n mri_watershed -rusage /Users/Matthew/Downloads/matt/ > mattmp/touch/rusage.mri_watershed.dat -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 20 T1.mgz > brainmask_T1_PFH20.auto.mgz \n > > \n mri_watershed -rusage /Users/Matthew/Downloads/matt/ > mattmp/touch/rusage.mri_watershed.dat -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 30 T1.mgz > brainmask_T1_PFH30.auto.mgz \n > > > > mri_watershed -rusage /Users/Matthew/Downloads/matt/ > mattmp/touch/rusage.mri_watershed.dat -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca > transforms/talairach_with_skull.lta -h 5 orig.mgz > brainmask_orig_PFH5.auto.mgz > > > > > > Mode: Use the information of atlas (default parms, --help for > details) > > Mode: Preflooding height manually specified > > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > > Referenced from: /Applications/freesurfer/bin/. > ./lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: /Applications/freesurfer/bin/. > ./lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > [... more of same ...] > > > > WARNING: Some multi-skullstrip operations may have failed! > > Continuing multi-skullstrip with the others... > > ERROR: failure in calculating best preflood height param. > > Darwin Matthews-MacBook-Air.local 17.5.0 Darwin Kernel Version 17.5.0: Mon > Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 > > > > recon-all -s mattmp exited with ERRORS at Thu May 3 12:57:24 EDT 2018 > > > > Attached is my log file for reference. Any suggestions appreciated. > > > > Cheers, > > > > -Matt > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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Scientific programmer position in neuroimage analysis and machine learning (University of Texas Southwestern, Dallas, USA)
by Albert Montillo 10 May '18

10 May '18

External Email - Use Caution Scientific programmer position in neuroimage analysis and machine learning (University of Texas Southwestern, Dallas, USA) The laboratory of Albert Montillo ( http://www.utsouthwestern.edu/labs/montillo ) in the Bioinformatics Department of UT Southwestern Medical Center is seeking a full time Scientific Programmer for studies of mental & neurodevelopmental disorders and neurodegenerative diseases. The Scientific Programmer will use multimodal MRI, and MEG/EEG data to study structural and functional circuit changes, and PET/SPECT, CT to study metabolic and pathophysiological changes associated with diagnosis and prognoses. The main responsibilities of the position include: implementing and optimizing image processing, computational and analyses pipelines for large-scale multimodal brain imaging data and corresponding clinical data. The lab is an interactive and collaborative team directed by Albert Montillo, Ph.D., conducting cutting-edge research to advance the theory and application of machine learning for the analysis of medical images. The lab addresses unmet clinical needs by forming predictive models that make diagnoses and prognoses more precise and advance neuroscience by furthering the understanding of mechanisms in disease and intervention. You will work directly with him and an array of principle investigators, collaborators and trainees. Medical image analysis software the lab has developed include machine learning-based methods for labeling structures throughout the brain (parcellation), versions of which are used worldwide and FDA approved. The lab has built deep learning methods to label networks in resting state fMRI and detect artifacts in MEG. The lab has pioneered deep learning decision forests that increase prediction accuracy while reducing prediction time and outcome prediction methods using advanced brain connectomics. Job responsibilities * Design, implement and optimize image processing, computational and analyses pipelines for large-scale multimodal brain imaging, including resting and task-based fMRI, diffusion MRI, PET/SPECT, CT, and MEG/EEG data on our high performance compute cluster. * Implement machine learning models to automate preprocessing, quality control, and computational data analysis of imaging, metabolic, genetic, behavioral, and clinical data. * Integrate third party pipelines with tailored in-house pipelines. * Build tools to organize and visualize the growing database of analysis results. * Contribute to writing of journal and conference papers. * Attend lab meetings, stay abreast of developments in image analysis and machine learning. * Coordinate data integration from ongoing studies. * Teach lab members about image processing steps, outputs and to quality control approaches. * A minimum three-year commitment is strongly encouraged. * Anticipated start date: immediate Experience of ideal applicants: * B.A. or B.S. Degree in Computer Science, Electrical Engineering, Biomedical Engineering or a related field with three (3) years scientific software development; Master's or Ph.D. preferred. Software development experience on high performance compute clusters or GPU-based machine learning is a strong plus. Will consider record of success in publishing computational results in lieu of experience. * Familiarity with at least 1 image data type: MRI, PET/SPECT, CT, MEG/EEG & format: NIFTI, DICOM. * Experience in at least 1 neuroimage analysis pipeline: NiPype, SPM, FSL, AFNI, FreeSurfer; for diffusion MRI: Camino, DTI-TK, DiPy, TrackVis, DTI/DSI studio, ExploreDTI; for MEG/EEG: Brainstorm, EEGLAB, FieldTrip, MNE, NUTMEG. * Experience developing image processing or image analysis software. Solid understand of standard CS data structures. * At least 2 years of experience in Linux; Python and 1 other language (Matlab, R, C/C++) * Practical ML experience applying at least 1 of the following: deep learning neural nets (RNN,CNN,DNN, UNet/VNet), DCGAN, deep reinforcement learning, transfer learning, autoencoders; classical or shallow machine learning; image/object recognition; time series analysis. * Experience in at least one of these Python libraries: Keras, scikit-learn, TensorFlow, PyTorch, Nilearn. * Experience in brain connectivity, graph theory, and genomic data analyses are significant advantages. * Optional but helpful: Experience in C/C++ (ITK library), cMake, software development. Familiarity with XNAT. Salary compensation is very competitive and enhanced by the low cost of living in Dallas. Benefits include health insurance. The candidate will also benefit from membership in vibrant national and international research communities through our on-going collaborations with UCLA, UCSF, UPenn, Stanford, Philips and Siemens Research, as well as a large local neuroscience communities through UTSW's O'Donnell Brain Institute, and UTD's Centers for Vital Longevity, Brain Health, and Brain Performance. Please apply by email to Dr. Montillo [Albert.Montillo(a)UTSouthwestern.edu] and include your CV and names and addresses of three references. Use the subject line "ScientificProgrammer: <your name>". The Montillo lab is co-located within the Bioinformatics Department on UT Southwestern's south campus and embedded in the Radiology Department on north campus. We are an integral part of the Advanced Imaging Research Center, and work closely with research groups within Neuroscience, Neurology, Psychiatry, Radiation Oncology, and Surgery. Montillo lab members have access to considerable computational resources, including the >6,800-core cluster with >8 Petabyte of storage available through UTSW's high-performance infrastructure (BioHPC - https://portal.biohpc.swmed.edu ). Future lab members will have the opportunity to work on a broad range of image analysis, machine learning and modeling on interdisciplinary teams, and participate in all aspects of method development, software implementation, data analysis, and validation with lab collaborators. Albert Montillo, Ph.D. Assistant Professor, Director, Deep Learning for Precision Health Laboratory Departments of Bioinformatics, Radiology and the Advanced Imaging Research Center University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8579 Albert.Montillo(a)UTSouthwestern.edu<mailto:Albert.Montillo@UTSouthwestern.edu> http://www.utsouthwestern.edu/labs/montillo UT Southwestern Medical Center is an Affirmative Action/Equal Opportunity Employer. Women, minorities, veterans and individuals with disabilities are encouraged to apply. ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Differences between qdec display and summary file for monte carlo corrected results
by yuanchao.zhang8＠gmail.com 10 May '18

10 May '18

External Email - Use Caution Hi, experts, I used qdec to do some analysis on my data and tried to correct for multiple comparisons using the button in qdec of monte carlo simulation. I saw only one big cluster in the display window of qdec. However, I saw three clusters in the terminal (printed text in the terminal) and in the .summary file. What is the problem here? Why is there the difference between the two? I also tried to visualize the result using freeview and loaded the mc-z.abs.th20.sig.vertex.mgh. I saw one cluster. but when I loaded the mc-z.abs.th20.sig.ocn.annot file, I saw three different clusters. It is confusing. Thanks a lot! Best, Yuanchao yuanchao.zhang8(a)gmail.com

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