Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

pre-smoothing coomand line
by Avideh Gharehgazlou 09 Feb '18

09 Feb '18

Hi Freesurfer experts, I found the answer to my previous question on FreeSurfer Wiki regarding pre-smoothing command line for LGI ( I am interested in looking at between-group differences in vertwex-wise LGI values). I am now aware that the following command line must be used: recon-all -s <subjid> -qcache -measure pial_lgi However, if I also want to look at surface area differences between groups later on, is using the above pre-smoothing command line correct? OR do I have to use the following command line considering that I Am not only looking at LGI values : recon-all -s <subjid> -qcache Would really appreciate your advice, Thanks, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Wm.mgz editing
by Emily Schwartz 09 Feb '18

09 Feb '18

Hi FreeSurfer community, I am relatively new to manually editing and am having some questions dealing with editing the wm.mgz. Occasionally, white matter and grey matter are being incorrectly cut out, but I cannot edit WM voxels in the area (lh postcentral) because they are already considered WM in the heat map (but excluded from the boundary). I have attached images. How would I go about fixing this? Would control points work here? And would the segmentation error in slices 79-81(lh postcentral) be edited by adding wm voxels (I can't really add any to slice 79)? (This is an elderly brain.) Thank you, Emily

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FW: Memorandum: Call for CASE Distinguished Postdoctoral Scholar {Disarmed}
by Anthony Dick 09 Feb '18

09 Feb '18

Hello, Please see below for a very time-sensitive opportunity for postdoctoral scholars in developmental neuroimaging in the Center for Children and Families (ccf.fiu.edu) Please contact me directly (adick(a)fiu.edu<mailto:adick@fiu.edu>) with any interest. Good salary/benefits in a great city (Miami, FL) and renewable for multiple years. Thanks! Anthony -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International University MM Campus AHC4 454 Department of Psychology and Center for Children and Families<http://www.ccf.fiu.edu/>, an FIU Preeminent Program<https://beyondpossible.fiu.edu/preeminent-programs/> 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu<mailto:adick@fiu.edu>; Webpage: http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the SSHD<http://www.sshdonline.org/> ##### Check out the new book<http://www.routledge.com/9781138960039>: Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis. From: Alina Delgado <alidelga(a)fiu.edu> on behalf of Michael Heithaus <heithaus(a)fiu.edu> Date: Friday, February 9, 2018 at 11:26 AM Subject: Memorandum: Call for CASE Distinguished Postdoctoral Scholar [cid:image001.png@01D320DC.8C56F780] MEMORANDUM To: All Faculty From: Michael R. Heithaus, Dean Date: February 9, 2018 MULTIPLE POSTDOCTORAL POSITIONS IN RESEARCH AREAS Florida International University is classified by Carnegie as a R1: Doctoral Universities - Highest Research Activity and recognized as a Carnegie engaged university. It is a public research university with colleges and schools<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> that offers 196 bachelor’s, master’s and doctoral<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…> programs in fields such as engineering, computer science, international relations, architecture, law and medicine. As one of South Florida’s anchor institutions, FIU contributes almost $9 billion each year to the local economy. FIU is Worlds Ahead in finding solutions to the most challenging problems of our time. FIU emphasizes research as a major component of its mission. FIU has awarded more than 220,000 degrees and enrolls more than 54,000 students in two campuses and three centers including FIU Downtown on Brickell, FIU@I-75, and the Miami Beach Urban Studios. FIU’s Medina Aquarius Program<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> houses the Aquarius Reef Base, a unique underwater research facility in the Florida Keys. FIU also supports artistic and cultural engagement through its three museums: Patricia & Phillip Frost Art Museum<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…>, the Wolfsonian-FIU<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…>, and the Jewish Museum of Florida-FIU<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage.c…>. FIU is a member of Conference USA<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…> and has more than 400 student-athletes participating in 18 sports. For more information about FIU, visit http://www.fiu.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__fiu.us1.list-2Dmanage1.…>. Position Title: Distinguished Postdoctoral Scholar Location: Florida International University, Miami, Florida Rank: Postdoctoral Research Associate Application Deadline: February 28, 2018 Description: The College of Arts, Science & Education<http://case.fiu.edu/> (CASE) at Florida International University (FIU), Miami, FL (USA) is seeking multiple candidates to serve as Distinguished Postdoctoral Scholars in fields of study relevant to CASE’s scholarly research areas in the sciences, humanities and education. Additionally, scholars may work with one of our preeminent centers including the Institute for Water & Environment, the Center for Children & Families, and the STEM Transformation Institute. The CASE Postdoctoral Scholars will work with a mentor/scholar of their choice. While the primary focus for the Postdoctoral Scholars will be to conduct scholarly activities and research, they will also be expected to interact with graduate students, participate in outreach efforts, and submit competitive research proposals where appropriate. The Postdoctoral Scholars will have the opportunity to teach if desired and will also be able to interact with faculty from across the College, as well as additional FIU faculty and external partners affiliated with the university. Appointments will have a term of one year starting in Summer or Fall 2018 and are renewable contingent upon excellent performance. The Scholar will receive a salary of $50,000, plus benefits and a discretionary fund of up to $5,000/year for research and travel expenditures. Applicants from underrepresented minority groups are highly encouraged to apply. Candidates will be selected based on demonstration of research excellence and potential future impact on their respective field of study. To apply, please send a cover letter that includes the name of the proposed faculty mentor, a proposed research plan, CV and the names of three references to alidelga(a)fiu.edu<mailto:alidelga@fiu.edu> . Please make sure you have contacted a potential supervisor who would be willing to be your mentor. [cid:image003.png@01D3A197.8B2B4A00]Cheers, Dr. Michael Heithaus Dean, College of Arts, Sciences & Education Florida International University

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smoothing command line- LGI
by Avideh Gharehgazlou 08 Feb '18

08 Feb '18

Hi, I am interested in looking at between-group differences in in LGI on Qdec (I will look at surface area as well later). I have a question regarding the smoothing stage. My recon-all for all subjects has completed, and I have LGI values for each subject. For smoothing, I was going to run the following command line: Recon-all –s <subjid> -qcache However, I saw in an archive post someone mentioning running the following line instead: recon-all -s <subjid> -qcache -measure pial_lgi Will you please tell me which command line I have to run? Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Cuda version > 5.0
by Melanie Ganz 08 Feb '18

08 Feb '18

Dear FS list, we just got a really nice graphics card (Quadro P6000) that we also would like to use to speed up recon-all, preferably for running high-res data with FS version 6. Now we know that in the precompiled FS version 6 it still looks for cuda 5.0, but it seems like some people have gotten it to work with 8.0 (see e.g. here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-May/052047.html) Has anyone gotten FS version 6 compiled with cuda 9.1? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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freesurfer segmentation: perirhinal Roi
by m.bahri＠uliege.be 08 Feb '18

08 Feb '18

Dear Freesurfer experts, We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin? Many thanks in advance, Best regards, -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.bahri(a)uliege.be Tel : + 32-4-3662304

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Re: [Freesurfer] Extending pial surface to include excluded cortex
by Arsenije Subotic 08 Feb '18

08 Feb '18

Hi Doug, I’ve noticed that in my right hemisphere on top (I’m only using this hemisphere as the other hemisphere has tissue loss due to ischemia) there is also some atrophy. However, I’ve noticed that the surface can still probably be extended. It seems that there are some wm voxels which connect and disconnect after a couple of slices when I have wm.mgz on top of brain mask and when I use the heat colormap. In this case, is it ok to add wm voxels to connect them to the wm.mgz volume? This is what the tutorial says I should do, but I am worried since the wm intensity is sometimes 0 between these detached wm voxels and the main wm voxel. You can see it on the top left corner. And in general if there is no white matter sometimes and the pial surface does not extend and there is no defect, what is the general protocol? Thank you for your help! Arsenije

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Extending pial surface to include excluded cortex
by Arsenije Subotic 07 Feb '18

07 Feb '18

Hi everyone, Is it possible to extend the pial surface in order to exclude some missing cortex, without adding control points? For one of my subjects I'm missing cortex for about 10-15 slices and I think control points should not be added. I've attached some screenshots that showcase the problem. Thanks for your help. Best, Arsenije

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brainGraph (graph theory analysis in R) major release: v2.0.0
by Chris Watson 07 Feb '18

07 Feb '18

Dear Freesurfer users, I am pleased to announce the 2nd major release of my R package for graph theory analysis of brain MRI data, "brainGraph". The main page on CRAN is at: https://cran.r-project.org/ web/packages/brainGraph/index.html The GitHub repository is at: https://github.com/cwatson/brainGraph *Installation* The latest version is already on CRAN for Linux distributions, and should be for Windows and Mac OS X soon (but there may be issues on non-Linux systems; see Chapter 1 of the User Guide). To install directly from CRAN: > install.packages('brainGraph') In the meantime (and for development versions), you may install from GitHub using the R package "devtools": > devtools::install_github('cwatson/brainGraph') *Getting help* The new User Guide has been completely overhauled, and now has a permanent link at: my GitHub Pages site (PDF warning) <https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Please start at the "Preface". You may also get help by opening an Issue <https://github.com/cwatson/brainGraph/issues> on the GitHub repository, or join the Google Group <https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>. *New features* You can find the release notes/changelog in NEWS.md, at: https://github.com/cwatson/brainGraph/blob/master/NEWS.md Major additions (since v1.0.0) that should be of interest include: - Vertex- and graph-level *mediation analysis* (chapter 11 of the Guide) - Multi-threshold permutation correction (MTPC) for GLM analyses (chapter 9) - Extension of GLM-based functions (including the *network-based statistic [NBS]* and MTPC) to allow for multiple contrasts in a single function call, and to allow for both T- and F-contrasts - Permutation/randomization is now done using the *Freedman-Lane algorithm* (as in *randomise* and *PALM*), although models are limited to simple GLM's - Introduction of R's *S3 classes* to simplify plotting and summarizing results - Calculation of a network's *s-core* membership - Calculation of network *communicability* and vertex *communicability betweenness centrality* Please let me know if you have any issues, bug reports, feature requests, etc. Chris Watson

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postdoctoral fellowship at Memory Disorders Research Center, VA Boston / Boston University
by Scott Hayes 07 Feb '18

07 Feb '18

Posting for a colleague, please see description below: POSTDOCTORAL FELLOWSHIP IN THE COGNITIVE NEUROSCIENCE OF MEMORY Memory Disorders Research Center, Boston University School of Medicine and VA Boston Healthcare System The Memory Disorders Research Center (MDRC ; https://www.bu.edu/mdrc/ ) is seeking a postdoctoral fellow in the cognitive neuroscience of memory to participate in both basic and translational cognitive neuroscience studies examining the role of the medial temporal lobes in future thinking and decision-making. In addition to behavioral and neuroimaging studies in healthy subjects and individuals with selective amnesia, this position offers the opportunity to be involved in a newly funded study on prospective cognition in PTSD. The MDRC is located in a medical center with state of the art imaging facilities, and affords many opportunities for interaction with other laboratories in cognitive and clinical neuroscience. The successful applicant will have a PhD in cognitive neuroscience, psychology, or closely related field, and experience in functional neuroimaging. Interested candidates should email a CV and letter describing their research experience and interests. Please also have three letters of recommendation emailed to Dr. Mieke Verfaellie (verf(a)bu.edu) Start date is summer 2018. Scott M. Hayes, Ph.D. Associate Director Neuroimaging Research for Veterans Center Memory Disorders Research Center VA Boston Healthcare System Assistant Professor of Psychiatry Boston University School of Medicine www.bu.edu/brainlab

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Freesurfer February 2018