Freesurfer

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30132 discussions

PET PVC transforms and MG voxels
by Adam Martersteck 07 Feb '19

07 Feb '19

External Email - Use Caution Hi FreeSurfer team, I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage paper: 1) It looks like the 2 rigid transforms created during mri_gtmpvc found at [$pvc_directory/aux/anat2bbpet.lta] and [$pvc_directory/aux/bbpet2anat.lta] are misnamed and the file names should be swapped. I noticed this isn’t a problem during mri_vol2surf (e.g. the PetSurfer wiki) because mri_vol2surf is “smart” and will automatically detect and invert the transform -- but it was causing problems for me when I used them during mri_vol2vol thinking the bbpet2anat.lta was from pet space to anat space. I apologize if you already knew about this – I couldn’t find anything in the FSv6 “Known Issues” or on the PetSurfer page. 2) I am using the MG PVC stream and a fairly conservative GM PVF threshold of 30% (similar to Doug’s paper). I noticed when the PVF is < 0.3 it sets the corrected [mg.nii.gz] image to zero in those voxels. Intuitively, I would have thought this would just “cap” all values < 0.3 to 0.3 and divide voxels by 0.3 to get a MG corrected voxel. I went back to Doug’s paper and found, indeed, the paper says, *“In this study, we varied the threshold from 1% to 50%. The TACs in voxels that did not meet this criterion were set to zero.”* So when I take the mg.nii.gz and use vol2surf as Doug did, I get a significant number of “patches” of zero values across the cortex (see attached image; every voxel along the normal is zero). I would then have smoothed this surface -- artificially lowering the entire neighborhood of vertices. Did you guys do something else for the Neuroimage paper when you were going from vol2surf? Or did you smooth the zeroes into the surrounding vertices? Maybe this isn't a problem in healthy brains and the projfrac 0.5 voxel is always a non-zero? Since I am working with significantly atrophied Alzheimer brains -- would “capping” the PVF make sense here to balance over correcting noise while avoiding non-zero vertices? Is there a command in fscalc to set all values between 0.0001 and 0.3 to 0.3 so I could do this? Thanks! Adam

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mri_label2label: some vertices mapped to nothing in target subject space
by Hengda He 07 Feb '19

07 Feb '19

External Email - Use Caution Hi Freesurfer Developers, I'm trying to map the vertices of a region (ex. caudal middle frontal) in one subject into the space of another subject (MNI) by using mri_label2label. I am using the freesurfer_dev/bin/mri_label2label.bin from freesurfer-x86_64-unknown-linux-gnu-dev5-20160513. For example, I have source Labels (aparc-lh-003_5thCol.label) , which are all in SurfaceRAS coordinates: #!ascii label , from subject FreeSurfer vox2ras=TkReg 8 104996 -35.679 16.281 25.156 1 104997 -36.480 16.439 25.362 2 104998 -37.443 16.702 25.369 3 105705 -41.554 16.840 28.930 4 105716 -40.445 17.153 28.046 5 105720 -39.570 17.200 26.959 6 131017 -29.315 12.915 45.422 7 131030 -31.304 12.514 46.455 8 By running this: /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh I got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label) 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 121253 -26.213 39.504 23.711 8.0000000000 Could I ask if there is a way to make sure that every vertex in the source '.label' file mapped to one vertex in the target subject space? For example, first two vertex (104996 -35.679 16.281 25.156 1) and (104997 -36.480 16.439 25.362 2) have no corresponded vertex in the target subject space. Best, Hengda

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mrs_glmfit error DOSS
by Michal Tanzer 07 Feb '19

07 Feb '19

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to compute mri_glmfit to correlate cortical thickness with my dependent var while controlling for age, gender, iq and MRIcenter (2 centers). I don’t have any interactions or assumptions on group differences so I am using DOSS design (with fsgd file) I have two questions regarding the analysis, which I couldn’t find in the archives ( I copied the error and attaching the fsgd file) When I am trying to control for the different variables using 4 classes (Center1Female, Center2 Female, Center1Male, Center2,Male) (Correlation matrix 0, 0 , 0 , 0 , 0, 0, 1) I am getting the error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y lh.ext.thickness.10.mgh --fsgd EXT2.fsgd doss --C EXT2.mtx --surf fsaverage lh --cortex --glmdir lh.ext2.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 1), Max=0.000000 (col 0) Column 1, all values are 0 -- However when I am not using the 2 sites as classes and using just the gender as a class (0,0,0,0,1) everything runs without errors. Is there any other way to control for the MRIsite? Thank you for your help with this matter Best wishes Michal -- Michal Tanzer, PhD Postdoctoral fellow; Clinical Psychologist. Research Department of Clinical, Educational and Health Psychology, University College London, United Kingdom

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applyMorph gives (10000 10000 10000) coordinates
by Peled, Noam 07 Feb '19

07 Feb '19

Hey all, I'm trying to morph patients' invasive electrodes into a template brain. I'm not sure why, but sometimes, the applyMorph gives me the (10000 10000 10000) coordinates for a subset of the electrodes, where the rest are ok. In the output, for those electrodes I can see it writes "not valid", but still gives reasonable coordinates and not (10000 10000 10000) For example: applyMorph --template /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz --transform /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d point_list /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt a Where in the output file you can see the (10000 10000 10000) coordinates. I attached the applyMorph output. btw, I'm using the Freesurfer dev version Thanks, Noam  LZ

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*** Call for PhD Applications ***
by Giada Lettieri 07 Feb '19

07 Feb '19

External Email - Use Caution *2019/20 PhD Programs at the IMT School for Advanced Studies LuccaDeadline for applications – April 23rd 2019, 12 pm CEST* Applications are now being accepted for the 2019/20 PhD Programs at the IMT School for Advanced Studies Lucca (*www.imtlucca.it <http://www.imtlucca.it>*), one of the six Schools of Excellence in Italy and one of the highest rated graduate schools in Europe according to the most recent U-Multirank survey. Highly motivated candidates from all disciplines are invited to apply for one of the 32 fully-funded scholarships within two doctoral Programs that integrate scientific competences of economics, engineering, computer science, neuroscience and behavioral psychology, physics, applied mathematics, statistics, history and sciences of cultural heritage. One of the four field-specific tracks is *Cognitive, Computational and Social Neurosciences*, which is under the “Cognitive and Cultural Systems” PhD Program. This research-based, multidisciplinary track focuses on cognitive, computational and social neurosciences, and integrates basic neuroscience methods, including molecular biology and genetics, with traditional experimental psychology and cognitive neuroscience. Students will attend multiple courses, including fundamentals in cognitive psychology, behavioral and social neuroscience, neuropsychology, psychophysiology, neural basis of perception, neural basis of consciousness, philosophy of science, critical thinking, structural and functional neuroimaging, and basic/advanced methods for data analysis. In particular, the CCSN track is designed to train researchers who will contribute to knowledge in (multi)disciplinary areas such as *multisensory perception, supramodality and cross-modality; sleep and consciousness; action recognition and motor control;neuroplasticity and learning; organization of semantic concepts; neurolinguistics; social and antisocial behavior; decision-makingprocesses in economics and financial environments; aesthetic perception*. During their doctoral studies, students are encouraged to carry out their research with the School’s Research Units. For conducting their experimental activities, students can rely on both in-house and outsourcing facilities. The IMT School has a Cyberphysics Lab equipped for behavioral, psychophysics and EEG (64 and 256 channels amplifiers) research. Functional and structural MRI studies can be conducted at any of the partner MRI scanner sites in Pisa (1.5 and 7 Tesla) and Massa (3 Tesla); EEG and fMRI acquisition could be combined. Courses are led by world-renowned researchers and provide students with all the theoretical skills and advanced tools required for rigorously tackling a multitude of analysis, design and management problems within the broad framework of systems analysis in economic, social, scientific, technological and cultural domains. Specialized faculty and staff create a network that provides key guidance and support throughout the PhD Program. Working closely with faculty, both in the classroom and in the development of research, students reach the highest levels of scholarly achievement. IMT School PhD graduates will be able to use the skills they acquired during their studies to recognize and resolve complex problems, to choose the most appropriate method or instrument to utilize when approaching these problems, even in disciplines outside of their primary field of research. All students are based in the recently restored San Francesco complex, a fully integrated Campus in the historical center of the beautiful Tuscan city of Lucca. The Campus includes renewed residential facilities, an on-site canteen, study and living rooms, a state-of-the-art library and outdoor recreational spaces, which foster a unique cultural, professional and social environment for our doctoral program. Eligible students, in addition to *free room and board*, will also receive a research scholarship which amounts to approximately *€15,300/year*. The scholarships are fully-funded for up to four years, with a possibility of graduating after the third year. The PhD Programs at the IMT School attracts students from around the world, providing a truly international environment. English is the official language of the School. Moreover, all students will have the opportunity to spend periods abroad at research institutes, laboratories or universities, both within the Erasmus+ framework and through ad hoc mobility agreements. Most IMT School PhD Graduates have reached prominent roles in academics, governmental institutions, public and private companies or professions across the globe. To find out more about the School, the admission requirements and how to apply, please see *https://www.imtlucca.it/en/programma-dottorato/overview <https://www.imtlucca.it/en/programma-dottorato/overview>* *Deadline for applications – April 23rd 2019, 12 pm CEST* -- *Giada Lettieri* PhD student Cognitive, Computational and Social Neuroscience *MOlecular MInd LABoratory <http://momilab.imtlucca.it/>* IMT - School for advanced studies Piazza S. Francesco 19, 55100, Lucca, Italy Mob: +39 389 0461034 <https://scholar.google.it/citations?user=ysqHTIwAAAAJ&hl=en>

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Announcing HCP Course 2019, July 8-12 in Portland, OR!
by Jennifer Elam 06 Feb '19

06 Feb '19

External Email - Use Caution We are pleased to announce the <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>2019 HCP Course: "Exploring the Human Connectome" <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…>, to be held July 8 – 12, 2019 at the University Place Hotel and Conference Center <https://www.uplacehotel.com/> at Portland State University in Portland, Oregon, USA. This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium. FreeSurfer is a major part of the HCP structural processing pipeline, has been critical to the processing of the HCP Young Adult project's over 1100 released high quality imaging datasets, and continues to be used in the processing of forthcoming Lifespan HCP data. The course is designed for those interested in: - using HCP-style data currently available from the young adult HCP and HCP Lifespan (Development and Aging) projects - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data (including legacy data) using HCP pipelines and methods - using Connectome Workbench <https://www.humanconnectome.org/software/connectome-workbench.html> tools and sharing data using the BALSA <https://balsa.wustl.edu/> imaging database - learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data forthcoming from large-scale projects currently collecting data (e.g., Lifespan HCP development and aging longitudinal data and Connectomes Related to Human Disease projects) - learning how to obtain data from the NIMH Data Archive (NDA) and setup processing in an Amazon Web Services (AWS) environment Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to students, postdocs, faculty, non-profit and industry participants. The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki> and Freesurfer <https://surfer.nmr.mgh.harvard.edu/> software. For more info and to register visit the <https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto…>HCP Course 2019 website <http://store.humanconnectome.org/courses/2019%20%20%20%20%20%20%20%20%20/ex…> . If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Portland! Best, 2019 HCP Course Organizers -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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Re: [Freesurfer] fs on GPU? Segmentation fault error!
by fsbuild 06 Feb '19

06 Feb '19

External Email - Use Caution Hello Vin, The latest/dev branch of freesurfer builds on Ubuntu 16 without cuda, but I have not tried compiling it for cuda on 16.04.  My understanding is that cuda builds are not officially supported.   I would first make sure that everything builds and runs w/o cuda. I would try not to manually copy/change the installation of cuda libraries,. i.e., if you need a specific version then I would install that version (rather than use the cp command to clobber version 5 with version 8, which may not be entirely backwards compatible and so could also cause run time errors).   If you know what you have for graphics/GPU hardware, then you should be able to lookup online what versions of cuda it supports, e.g., for Nividia hardware, https://developer.nvidia.com/cuda-gpus You can also get a currently supported cuda version to install for Ubuntu 16.04 from this link, https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch… - R. vin rasa February 6, 2019 at 12:17         External Email - Use Caution        Freesurfer Wizards, Any thoughts on this? Thanks in advance ## I renamed: /usr/local/cuda-8.0/lib64$ sudo cp libcudart.so.8.0 libcudart.so.5.0 in the next step: recon-all -i $sub_dir/$i/"$i".nii -all -sd $output_dir $i -use-gpu.. Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 9.20 Runtime : 8.0 Acquiring CUDA device Using default device CUDA device: TITAN Xp Segmentation fault Linux Dond-12 1.25.0-13-generic #36~16.04.1-Ubuntu SMP Wed Aug 15 17:21:05 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2 exited with ERRORS at Mi 6. Feb 18:14:50 CET 2019 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer TRACULA with FAD
by Alex Dufford 04 Feb '19

04 Feb '19

External Email - Use Caution Hello Freesurfer experts, I am interested in running an along the tract analysis with the outputs from tracula. I am interested in using https://www.nitrc.org/projects/fadttster/ to do so. I was wondering where to find the 'arc length' for the fibers and if there is anything else I should consider in try to analyze the fibers with FADttster. Thank you! Best, Alex -- Alexander Dufford M.A. Developmental Psychology Graduate Student Family and Child Neuroscience Laboratory University of Denver Office Phone: 303-871-3096 http://www.du.edu/ahss/psychology/fcnlab/

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(no subject)
by Jordan Fowler 04 Feb '19

04 Feb '19

External Email - Use Caution Here is the message displayed: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Jordans-MacBook-Air-2:~ jordanfowler$ > cp $FREESURFER_HOME/subjects/sample-001.mgz . -bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied

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free surfer install issues
by Jordan Fowler 04 Feb '19

04 Feb '19

External Email - Use Caution I have recently installed the free surfer software and when testing that it is installed correctly using the examples listed on the website I get a permission denied message. How can I go about fixing this? Attached is the terminal output from trying to run the first example. Thank you, Jordan Fowler

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