Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

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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Projecting meta-analytic map on the surface
by srishti goel 09 May '18

09 May '18

External Email - Use Caution Hello Freesurfers, I have a network based map that has been produced from a meta analysis using NeuroElf on the standard colins template. I want to project this map on the surface of an MNI template. Does anyone have thoughts about how that could be achieved? 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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mri_vol2surf
by Abdullah Ishaque 09 May '18

09 May '18

External Email - Use Caution Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses. Here's what I've done so far: 1. recon-all for all the subjects 2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space) The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful! Let me know. Thanks!

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inherent smoothing
by Joost Janssen 09 May '18

09 May '18

External Email - Use Caution Dear Doug, I'd like to determine the inherent smoothing of ?h.thickness in my sample. What is the best way to do this? Thanks, -joost

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