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X11 / mesa update broke tkmedit snapshots
by Flavin, John 22 Jun '16

22 Jun '16

Hi all, I run the pipelines for the CNDA and various other XNAT installations. We recently updated some of our packages, and our Freesurfer snapshots (generated with tkmedit using a tcl script) have broken. We're on Centos 6.8. The package that seems to cause the breakage is one of the mesa packages, probably mesa-libGL, upgraded from 10.4.3 to 11.0.7. (But it's hard to be sure that's the exact one because of the dependencies.) That mesa package gets pulled in as a dependency to an X11 update, specifically xorg-x11-server-Xorg upgraded from 1.15.0 to 1.17.4. We're working now on figuring out a strategy to downgrade these, and some others. It's a little hairy because there are a lot of dependent packages and a lot of affected machines. If anyone else has seen this, or knows how to fix it, I'd love to hear from you. John Flavin ________________________________ 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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Viewing Select Labels
by badji atef 22 Jun '16

22 Jun '16

Hello, I tried to do the quick tutorial to be able to see specific anatomic region i.e the corpus callosum,I highlighted the aparc+aseg file and changed the threshold number with low=253 and high=255 but I don't get the same results at all. Should I change the frame too?and what about the replace In value with or replace Out value with ? FreeviewAnatomicalVolumes

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New Research Assistant Position in Neuroimaging Available at Washington University in St Louis
by Karl Friedrichsen 22 Jun '16

22 Jun '16

NEW RESEARCH ASSISTANT POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a research assistant position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Results are expected to have broad implications not only for understanding the pathophysiology of neurodegenerative disorders but more generally for understanding the relationship between brain physiology, anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic resonance imaging (MRI) research facilities and has an outstanding record of productivity. Funding is guaranteed for a minimum 2 year commitment PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research assistant will be to archive/organize images (large multi-modal imaging datasets) and process/analyze multi-modal neuroimaging data. The research assistant will assist in various lab maintenance and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. QUALIFICATIONS: The qualified candidate will have at least a Bachelor's degree in human biology, neurosciences, psychology, bioengineering, computer sciences, or other related fields. The qualified candidate must have computer skills and some basic knowledge of computer languages (e.g. C, C++, Matlab, Python). The research assistant must be dependable, have good attention to details, be well organized, self-motivated, and comfortable working as part of a team. Previous experience with fMRI data analysis programs is preferred but not necessary. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110

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New Post Doctoral Position in Neuroimaging Available at Washington University in St Louis
by Karl Friedrichsen 22 Jun '16

22 Jun '16

NEW POST DOCTORAL POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a post doctoral position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Results are expected to have broad implications not only for understanding the pathophysiology of neurodegenerative disorders but more generally for understanding the relationship between brain physiology, anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic resonance imaging (MRI) research facilities and has an outstanding record of productivity. Writing manuscripts and applying for independent grants will be strongly encouraged. Funding is guaranteed for a minimum 2 year commitment. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the post-doctoral fellow will be to conceive, design, and analyze studies pertaining to the effect of neurodegenerative disease on structural (e.g., volumetric imaging and diffusion tensor imaging [DTI]) and functional (e.g., blood oxygen level dependent [BOLD] imaging and arterial spin labeling [ASL]) brain organization. Anticipated activities entail development and implementation of new analytic strategies to facilitate understanding of disease in the human brain, integration of large multi-modal imaging datasets, and analysis of the relationship between brain imaging markers and cognition or clinical status. Strong written communication skills are required. Attention to detail, organizational capability, and the ability to handle multiple concurrent tasks are essential. The post-doctoral fellow is expected to be able to work independently as well as part of a team in a fast paced environment. PREFERRED EDUCATION/EXPERIENCE: A PhD in neuroscience, computer science, physics, engineering, mathematics, psychology, or related fields is requested. Previous experience is preferred in computational methods, scientific programming, and/or neuroimaging data analysis. Experience in computer programming (e.g. Matlab, shell scripting, Python, C), image processing (e.g. custom routines, FSL, AFNI, Freesurfer), and statistical analyses (R, SPSS) is beneficial. CRITICAL SKILLS AND EXPERTISE: The successful applicant will have a strong background in scientific computing (e.g., Unix/Linux experience). Academic proficiency in statistics is strongly desired. The applicant should have experience designing or adopting statistical approaches to address neurobiological questions. Preference will be given to applicants with a strong publication record or experience with writing grant applications. The successful candidate should be highly motivated with excellent analytical and interpersonal skills. To apply, please send a letter of interest and CV to bances(a)wustl.edu. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 bances(a)wustl.edu

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Quality control with different pipelines
by Kirstie Whitaker 22 Jun '16

22 Jun '16

Hi everyone, I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released). If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does? Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits? Thank you again for the fantastic tools! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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LGI
by Walid Yassin 22 Jun '16

22 Jun '16

*Hello,* *I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error!* ******************************************************* Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! ******************************************************* *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* ******************************************************* function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); ******************************************************* *Which i did, but i am still getting this error!* *Any recommendations on what to do next? I am running MATLAB_R2016.* *Thank you in advance,* *WY*

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aseg mask error
by Jasmin Alves 22 Jun '16

22 Jun '16

FREESURFER_HOME: /home/rcf-proj/kap/shared/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.22.1.el6.x86_64 x86_64 Hello Freesurfer, For some strange reason, a participant's entire aseg is being mapped onto one hemisphere. This is the case with two different mprage files. I have attached a screenshot. I am not quite sure how to fix this. Is it something I should fix using TKMEDIT? Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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cortical surface pattern matching
by GREGORY R KIRK 21 Jun '16

21 Jun '16

Hi, has anyone created functionality to compare the spatial correlation/similarity of two patterns in the form of cortical surface overlays. What I am looking at is a have scalar at every point on the cortical surface. obviously this is just a list of vertices with a scalar value associated with each. obviously I can map these both onto an average cortical surface and then simply compute the correlation of both of these. but of course pattern similarity is an inherently spatial problem and for cortical surfaces a 2 dimensional spatial correlation or other similarity metric would be what you want. Here the order of vertices in a vertex list maps somewhat like a string around the cortex and so the next wrap around you have vertices which are adjacent on the surface but distant by the metric of vertex count. is there any implementation of a similarity metric which takes this coordinate problem into account. In my measure every vertex across both hemi has a value and so i am not interested in something for a small localized patch. any thoughts appreciated Greg

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XQuartz 2.7.9 update results in errors
by Kate Mills 21 Jun '16

21 Jun '16

Hi All, My lab is having difficulty loading the freeview gui after updating to the latest version of XQuartz (2.7.9). We were wondering if others have experienced this issue? We have reverted by to XQuartz 2.7.8 on our machines for now. In case relevant, this errors seems to span Mac OS versions. Thank you! Kate

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smoothing T1 images
by John Anderson 21 Jun '16

21 Jun '16

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