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Job post: full-time research assistant in the lab of Dr. Emily Finn, Dartmouth College
by Emily S. Finn 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfer users, The laboratory of Dr. Emily Finn in the Department of Psychological and Brain Sciences at Dartmouth College is seeking a full-time Research Assistant for a targeted start date of July 2020. The research of the lab focuses on individual differences in brain activity and connectivity, and how these relate to behavior. Some key questions are: How do our intrinsic traits bias our perceptions and judgments, and how is this reflected in patterns of brain activity? Why might different people arrive at different interpretations of the same experience? Our research combines behavioral, neuroimaging and computational modeling techniques to study individual differences in cognition, especially under rich, dynamic, “naturalistic” stimulation such as watching movies or listening to stories. This position is especially well-suited for individuals planning to apply for a PhD in cognitive neuroscience or psychology. The position would be for an initial 1 year, with an ability to renew up to 2 additional years thereafter based on performance. Preference will be given to applicants who are willing to stay at least two years. Questions may be directed to Emily Finn (emily.s.finn(a)dartmouth.edu) For full consideration, please apply by March 13, 2020. Position Purpose Plays a crucial role in helping to set up the lab as well as conduct experiments. The Research Assistant’s role will involve administrative tasks, such as purchases, participant recruitment, ethics applications, organizing files, and setting up meetings. Conducts research, including designing experiments, collecting data, analyzing data, and writing papers, with the aim of completing an independent research project by the end of their time. The Research Assistant will learn techniques in programming, functional MRI brain scanning, and in-person and online behavioral experimentation. Required Qualifications - Bachelor’s degree with a major in psychology, neuroscience, cognitive science, computer science, biology, or a similar field - Previous experience in one or more laboratory methods, procedures and techniques as well as the equipment and instruments, e.g., fMRI data acquisition, eye-tracking, behavioral experimentation - Ability to work independently and apply critical thinking and sound judgment - Excellent organizational and time management skills - Knowledge of software for writing and presentation (e.g., Microsoft Office), and online scientific literature search engines Preferred Qualifications - Two years of relevant laboratory/ research experience during undergraduate - General programming and computational skills for data analysis (e.g., Python, MATLAB, R) - Experience with neuroimaging analysis software (e.g., AFNI, SPM, FSL) and experiment creation (e.g., PsychoPy, Psychtoolbox) - Experience working with human participants For more information or to apply: https://searchjobs.dartmouth.edu/postings/53845 -- Emily S. Finn, PhD Assistant Professor, beginning July 2020 Psychological & Brain Sciences Dartmouth College esfinn.github.io<http://esfinn.github.io>

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Full analysis chain without Topology fix, Talairach check?
by HsuD3＠mskcc.org 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfers, I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain. Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it? I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs. For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me. Best regards, Dylan Hsu, Ph.D Memorial Sloan-Kettering Cancer Center [1] <https://github.com/freesurfer/freesurfer/tree/dev/scripts#L3128-L3139> https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f… ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

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Segmentation problem
by Marina Fernández 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina.

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Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
by fsbuild 26 Feb '20

26 Feb '20

External Email - Use Caution You also see a list of packages to install on the freesurfer wiki pages under, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements - R. On Feb 26, 2020, at 12:03, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Hi Tim,try: wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1u… dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.debMore details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-…. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn February 26, 2020 at 5:36 PM "Harrigan, Timothy P." <Timothy.Harrigan(a)jhuapl.edu> wrote:       External Email - Use Caution        HI,I'm setting up freeview on a Linux 18..04 system and running through the instructions inhttps://surfer.nmr.mgh..harvard.edu/fswiki/DownloadAndInstallI got through to Example 4: "View the output volumes..."  and got the error below.harritp1@TPHTVB:~/FSSubjects$ freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryIt looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e.  sudo apt-get install -y libpng-dev but that didn't fix the problem.Have you dealt with this?ThanksTimTimothy P. Harrigan ScDResearch and Exploratory Development DivisionJohns Hopkins University Applied Physics LaboratoryPhone: 240-228-5943Cell/Text: 240-280-9444_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
by Harrigan, Timothy P. 26 Feb '20

26 Feb '20

External Email - Use Caution HI, I'm setting up freeview on a Linux 18.04 system and running through the instructions in https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I got through to Example 4: "View the output volumes..." and got the error below. harritp1@TPHTVB:~/FSSubjects$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory It looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem. Have you dealt with this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444

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Re: [Freesurfer] Qdec not running ("image not found" error message)
by fsbuild 26 Feb '20

26 Feb '20

External Email - Use Caution Hello Alex, It looks like you need to install Xquartz on your Mac with the X Windows libraries including libGLU.1.dylib. Download from here, open and run the installer package. https://www.xquartz.org/ - R. On Feb 25, 2020, at 23:27, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn(a)email.gwu.edu> wrote:        External Email - Use Caution        Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec &- Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib  Referenced from: /Applications/freesurfer/bin/qdec.bin  Reason: image not foundAbortAny ideas on how I could fix this? Thanks! All the best, Alex _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Qdec not running ("image not found" error message)
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 25 Feb '20

25 Feb '20

External Email - Use Caution Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec & - Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Abort Any ideas on how I could fix this? Thanks! All the best, Alex

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why topology fix almost takes 4 days to finish job
by Frank Robert 25 Feb '20

25 Feb '20

External Email - Use Caution Hello freesurfer experts I am using freesurfer to run recon-all, recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image It takes about 5 days to finish the process. I find that the most time consuming process is topology fix, it almost takes 4 days for L and R side of hemisphere. I checked the manual, it is supposed to take 1-9h to finish. Do you know why? I think my data set may have a relatively large ventricles ( of course, it is not so large). I put the flags --bigventricles and --parallel, it still takes about 3 days to finish. but if I use recon-all -i T1_MPRAGE image rather than recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image. It will take about 15h, why this make such big difference? Many thanks. Frank

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Read Freesurfer surfaces and annotation files in C++
by Michael Jordan 25 Feb '20

25 Feb '20

External Email - Use Caution Hi, there are some easy to use Matlab/Python functions to read/write native Freesurfer files (.annot, surfaces etc.) available. Anyone knows something similar for C++ (VTK)? Thank you.

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Question about skull strip error
by Vicky Shi 25 Feb '20

25 Feb '20

External Email - Use Caution Dear Freesurfer expert, I ran recon-all on one subject and part of the cortex was excluded. I followed the FS tutorial to change the watershed preflooding height percentage by using the command below: recon-all -skullstrip -wsthresh 30 -clean-bm -subjid <subject name> The new brainmask file did include all cortex but contain some non-brain tissue (tissue around spinal cord) as well. Then I want to regenerate the aseg.mgz file. So I redo the recon-all command like below: recon-all -all -subjid <subject name> The brainmask output was still like the old one, excluding part of cortex. The new reconstruction seems not use my edited brainmask.mgz. My question is: Do I need to add some flag in recon-all to make sure it use new watershed value/ edited brainmask.mgz? And how I can exclude the non-brain part in the brain mask while keeping all brain part? Simply changing the watershed value didn't do the work well. Thank you so much for your help! Vicky

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