Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Job posting: Research assistant Z-lab @OSU
by Saygin, Zeynep M. 17 Mar '23

17 Mar '23

External Email - Use Caution Dear all, I'm hiring a full-time research assistant. Please see below! The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to assist with neuroscience research on the functional and structural architecture of the human brain in adults and children. The Z-lab studies the functional and structural differentiation of the human brain across early development and adulthood, and the plasticity of the brain in response to disorders and injury (see zeynepsaygin.com<http://secure-web.cisco.com/1ztPG91tT0rU15cgdGalf9OPqTrW94SE7CF8G3hNXs9CfHA…> for recent publications). Please apply here: https://secure-web.cisco.com/1sWjkkfC4POCU7eVOCKoEI1dfwLHm5ZVKy_C14DQGA1Q3r… Review of applications will continue on a rolling basis until the position is filled. The target start date is July 2023 but this is negotiable. This is a 1-year position with the possibility for renewal contingent on performance and funding. The Project Coordinator will oversee and execute data collection for ongoing studies in the lab, hire and oversee undergraduate research assistants, manage administrative study materials, and helping analyze study data. This position is an excellent opportunity for an enthusiastic individual looking to gain research experience on related topics (development, cognitive neuroscience, psychology, brain injury) before applying to graduate or medical school. Responsibilities will include: * Overseeing and executing recruitment and retention of infant, child, and adult participants * Overseeing and executing data collection (including neuroimaging & behavioral assessments & experiments) * Managing lab materials, including: preparing and managing IRB protocols, study protocols, training materials; conducting literature reviews; maintaining and supporting website and github pages (including updating with datasets and analysis scripts/software). * Working with lab members and collaborators to collect and analyze data; hiring and overseeing undergraduate research assistants; training new staff members on study protocols; organizing progress meetings; cultivating diverse, inclusive, and collaborative workplace. * Attending and presenting at research conferences and co-authoring manuscripts. REQUIRED QUALIFICATIONS: * Bachelor's degree (preferably in psychology, neuroscience, cognitive science or related field). * Exceptional interpersonal skills and cultural sensitivity for interacting with infants, children, and parents from diverse backgrounds. * Candidate must be able to travel for recruitment, meetings, and data collection. * Strong organizational and time management skills, motivation to learn new skills, and determination to achieve study enrollment targets. PREFERRED QUALIFICATIONS: * Previous experience interacting with infants or families from diverse backgrounds. * Previous research experience (working with human subjects data; behavioral or neuroimaging) and/or coding experience (e.g., MATLAB, Python, shell scripting). Interested individuals should contact saygin.3(a)osu.edu with a CV and names of 2-3 references. -- Zeynep M. Saygin, Ph.D. Assistant Professor of Psychology The Ohio State University 205 Psychology Bldg. 1835 Neil Ave Columbus, OH 43210 zlab<http://secure-web.cisco.com/1ztPG91tT0rU15cgdGalf9OPqTrW94SE7CF8G3hNXs9CfHA…>

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Help passcode
by Isra RM 17 Mar '23

17 Mar '23

External Email - Use Caution Hello FreeSurfer, Where can I find a passcode to unzip the VW file FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded? Thanks

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Re: [Freesurfer] Transparency issue in FreeView
by fsbuild 17 Mar '23

17 Mar '23

External Email - Use Caution My guess is remote rendering via ssh uses a different set of drivers compared to rendering done sitting at the console of the CentOS8 machine.  Usually it is remote rendering that is broken more often than not because of differences in OpenGL drivers or the graphics card on the machine ssh’ing in receiving X11 forwarding, e.g. OpenGL trying to work in headless mode. Either way, you can try setting  LIBGL_DEBUG=verbose to see what’s reported and/or different between the local and remote environments.$ export LIBGL_DEBUG=verbose… or just on the command line when you run the command …$ LIBGL_DEBUG=verbose  freeview <arguments> Graphics card drivers from vendors like NVIDIA can modify system libGL libraries and some people have found that for (remote) rendering to work those drivers need to be uninstalled.  I have not heard of that adversely affecting rending from the host machine’s console however.  But you might want to check you have the latest OpenGL drivers installed on the CentOS8 machine, e.g., https://secure-web.cisco.com/1B4t-A6P6PLfb6I410WFHd2fC2dzFjhrrZd… This article is more geared towards remote debugging, but might give you some insight, https://secure-web.cisco.com/1PiPDkNychDnnDz-TlUKIX15aBjhCgC8… - R. On Mar 16, 2023, at 19:19, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi All,I have a colleague who is trying to use FreeView on Red Hat Enterprise Linux 8, and there seems to be a transparency issue where windows behind the viewer are being displayed.  See attached screenshot.This only happens when using FreeView on the desktop.  When using freeview over `ssh -X` everything looks good.Any ideas, or debugging info we could pass along?Thanks,-Paul<Screen Shot 2023-03-16 at 4.17.47 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_synthseg ERROR 'std::bad_alloc'
by fsbuild 17 Mar '23

17 Mar '23

External Email - Use Caution Various postings reference it’s related to the application failing to obtain memory.  That does not necessarily mean virtual/physical memory is exhausted, but rather the memory management scheme used by the application is unable to provide a big enough chunk of memory to be allocated in time for use.   Some people suggest monitoring the process, e.g., “ps” command, to look at either system memory usage or GPU memory usage in the case of using GPU, e.g., NVIDIA command “nvidia-smi” while things are running.  One post seems to indicate memory is not physically underrun from a graph of memory consumption when the error occurs. - R. https://secure-web.cisco.com/1lQSEMDdo1ulf5k6B_UJrBUyBSDW206IbKCm6lAKEaSvRW… https://secure-web.cisco.com/167ERnV8gwZmPGQneh48CAQ4nbl0Jx8bfLYgpOKuUmdUIe… https://secure-web.cisco.com/1PBtw1Ekc9zECMksHeg_KIzO-vNIHFECQ7w13UbgUebvky… https://secure-web.cisco.com/1CxLDSwk7AAkcqahJRoHD9KM8_J8VZB04y-dz5oD-weCfr… On Mar 17, 2023, at 05:37, Steinbacher Jürgen <j.steinbacher(a)salk.at> wrote:        External Email - Use Caution        Dear Freesurfer team, I have now fs 7.3.2 installed on ubuntu 22.04.2 on a 8 core i7-4790 CPU (supporting AVX instructions)  with 28.0Gb  fs works fine now,  but I had a patient where the segmentation did not work  well, so I wanted to try  mri_synthseg.I have tensorflow 2.4.1 (python 3.7.13) installed and running on a gtx 1650 gpu. So running mri_synthseg first time did not prompt to install it again.When I run mri_synthseg  it tells predicting 1/1 and after about 25 sec it terminates telling: „terminate called after throwing an instance of ‚std::bad_alloc‘“  what(): std::bad_alloc  Abort(core dumped)?????????? (memory problem??)It terminates independent of using other patients, or gpu – cpu or more or less cores..I also tried „synthstrip“ to test the tensorflow installation working with fs and this works well!Do you have an idea, & solution??? Greetings Jürgen _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_synthseg ERROR 'std::bad_alloc'
by Steinbacher Jürgen 17 Mar '23

17 Mar '23

External Email - Use Caution Dear Freesurfer team, I have now fs 7.3.2 installed on ubuntu 22.04.2 on a 8 core i7-4790 CPU (supporting AVX instructions) with 28.0Gb fs works fine now, but I had a patient where the segmentation did not work well, so I wanted to try mri_synthseg. I have tensorflow 2.4.1 (python 3.7.13) installed and running on a gtx 1650 gpu. So running mri_synthseg first time did not prompt to install it again. When I run mri_synthseg it tells predicting 1/1 and after about 25 sec it terminates telling: "terminate called after throwing an instance of 'std::bad_alloc'" what(): std::bad_alloc Abort(core dumped) ?????????? (memory problem??) It terminates independent of using other patients, or gpu - cpu or more or less cores.. I also tried "synthstrip" to test the tensorflow installation working with fs and this works well! Do you have an idea, & solution??? Greetings Jürgen

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CT and mri_synthsr
by Gonzalo Rojas Costa 16 Mar '23

16 Mar '23

External Email - Use Caution Dear Juan: I tested mri_synthsr using three different CT images using the threshold (80 value) that you told me some days ago. The first works ok, but with the other 2, I got the following error: developer@developer-VirtualBox:~$ mri_synthseg --i /home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

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Transparency issue in FreeView
by Wighton, Paul 16 Mar '23

16 Mar '23

Hi All, I have a colleague who is trying to use FreeView on Red Hat Enterprise Linux 8, and there seems to be a transparency issue where windows behind the viewer are being displayed. See attached screenshot. This only happens when using FreeView on the desktop. When using freeview over `ssh -X` everything looks good. Any ideas, or debugging info we could pass along? Thanks, -Paul

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request
by Isra RM 16 Mar '23

16 Mar '23

External Email - Use Caution Dear FS team I would like to request the passcode to the VM FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded Thanks in advance Isra RM

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Question on EasyReg forward field
by Codrin Mironiuc 16 Mar '23

16 Mar '23

External Email - Use Caution Hi, I am trying to shift the statistical maps that I obtained from a second-level fMRI analysis (meaning across multiple sessions for one subject). My plan is to use EasyReg to align the functional data to the structural data. Based on the resulting field then I intend to use it to shift the statistical maps using mri_easywarp. I know that for EasyReg, it doesn't matter the order in that I provide the arguments, e.g. Order 1: mri_easyreg --ref <structural_image> --flo <functional_image> Would produce the same result as Order 2: mri_easyreg --ref <functional_image> --flo <structural_image> Nevertheless, I believe that depending on whether I choose 'Order 1' or 'Order 2', I would need a different field to allign the statistical maps, would this be correct? I think that if I choose Order 1, then the backward field is needed, whereas if I choose Order 2, I would need the forward, field, right? Or would it be the forward field for both Orders that is needed in order to allign the statistical maps from the second level (across runs for a single subject)? Many thanks!Codrin

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Question on easy reg
by Codrin Mironiuc 16 Mar '23

16 Mar '23

External Email - Use Caution Hi, I have tried to use the EasyReg package to obtain the forward field by registering a functional slab to the structural (with skull) of a subject.This doesn't seem to work, do you know what may be the issue? Many thanks,Codrin

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Freesurfer March 2023