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Research technician opening at Wash U Neurology
by Yendiki, Anastasia 26 Jan '18

26 Jan '18

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING POSITION SUMMARY: Applications are invited for a research technician at Washington University in St. Louis. This well-established laboratory studies the structural and functional organization of the human brain using multi-modal imaging: including magnetic resonance imaging (MRI) and positron emission tomography (PET). The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Benefits of this position include: 1) Involvement in cutting edge research performed by a leading neuroimaging research laboratory 2) Potential to be involved as an author on manuscripts 3) Potential to present results at national and international conferences 4) Ability to attend talks and lectures in the field. Funding is guaranteed for up to 2 years. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research technician will be to archive/organize images (large multi-modal imaging datasets) and process neuroimaging data. The technician will study how disease affects the human brain by integrating large multi-modal imaging datasets and analyzing the relationship between brain imaging markers and clinical status. The technician will assist in various lab maintenance, transfer of files, database management, and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. Qualifications: The qualified candidate should 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 knowledge of computer languages (e.g. Matlab, Python, shell scripting in CSH or BASH). The research technician must be dependable, have good attention to details, be well organized, be self-motivated, and be comfortable working as part of a team environment. Previous experience with neuroimaging data analysis programs is preferred but not required. 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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Re: [Freesurfer] Hippocampus Subfield analysis error
by Shan Hannah Luo 26 Jan '18

26 Jan '18

Hi Andrew, thanks for your reply. Yes, I am using bash and my operating system is Mac OS X 10.9.5. Could you direct me how to set a path correctly? I ran recon_all fine. On Wed, Jan 24, 2018 at 1:14 PM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Hannah, > > > > What kind of environment are you running this in? These errors make it > seem like you do not have a PATH variable set at all. Are you using bash? > and what operating system? > > > > best > > Andrew > > > > > > > On Jan 22, 2018, at 4:06 AM, Iglesias Gonzalez, Eugenio < > e.iglesias(a)ucl.ac.uk> wrote: > > > > > > Hi Hannah, > > > This seems like a more general problem with your PATH, but I’m sure > Andrew (CCed) has a better idea of what might be going on. > > > Cheers, > > > /Eugenio > > > > > > -- > > > Juan Eugenio Iglesias > > > ERC Senior Research Fellow > > > Translational Imaging Group > > > University College London > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > jeiglesias.com&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r= > KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s= > h744EAFP3ZR0HURi0cl4du0JQime2YET6lIh-INZJcs&e= > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__cmictig. > cs.ucl.ac.uk_&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r= > KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s= > ovG8neKhH3sGEwGqRi5OeKX-E4aLdh0zeuZYBniwaG0&e= > > > > > > > > > On 20/01/2018, 00:23, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf > of Hannah's USC Email" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf > of shanluo(a)usc.edu> wrote: > > > > > > > > > Hi Freesurfer experts, > > > > > > I tried to do hippocampus subfield analysis but failed. I got this > error message: > > > > > > #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 > 15:27:36 PST 2018 > > > dirname: Command not found. > > > pwd: Command not found. > > > pwd: Command not found. > > > /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. > > > #-------------------------------------------- > > > #@# Hippocampal Subfields processing (T1 only) right Fri Jan 19 > 15:27:36 PST 2018 > > > dirname: Command not found. > > > pwd: Command not found. > > > pwd: Command not found. > > > /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. > > > > > > Your help would be greatly appreciated. Thanks! > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. > nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c= > clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=KJthMqWw4OBi4XmtFDLHhQ&m= > ZaKfBrAuyRsXIKre92fMvvPb77h_SvySEbgBUJOgLiM&s=nAlemdWlQJCLxi_63U- > PEBEjbULXp2FaLQA0GUgzi6Q&e= > > > > > > > > > The information in this e-mail is intended only for the person to > whom it is > > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > > contains patient information, please contact the Partners Compliance > HelpLine at > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > partners.org_complianceline&d=DwIGaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN > 0H8p7CSfnc_gI&r=KJthMqWw4OBi4XmtFDLHhQ&m=ZaKfBrAuyRsXIKre92fMvvPb77h_ > SvySEbgBUJOgLiM&s=-EJZERU1tZAo0E9Ma0DrkvnV70qUsZwJPStubsuwxEU&e= . If the > e-mail was sent to you in error > > > but does not contain patient information, please contact the sender > and properly > > > dispose of the e-mail. > > > > > > > > > > > > >

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gtmpvc output stat result in negative uptake value
by Chakmeedaj Sethanandha 26 Jan '18

26 Jan '18

Dear Freesurfer experts, We found that a stat file in gtmpvc output folder shows that one area has negative avg uptake value. What could explain this result? Quoted the row from the file: 11 26 Left-Accumbens-area subcort_gm 3 2.351 -0.490 2.3033 The command used is as in the log file. Best regards, Jak

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PetSurfer: Other quantification algorithms?
by Elijah Mak 25 Jan '18

25 Jan '18

Dear Doug, In addition to the MRTM approaches, I was wondering if you have any plans to implement other algorithms in PetSurfer, such as supervised cluster analysis for extracting reference tissue activity? I am working with [11C]PK11195 PET data (neuroinflammation), for which there is no suitable reference region in neurodegenerative conditions. Hope to get your take on this please. Thanks very much. Best Wishes, Elijah

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Tracula
by Nicole Mckay 25 Jan '18

25 Jan '18

Hi all, I have previously run full diffusion preprocessing using FSL and would like to now use tracula to construct the paths. Is it possible to input my already processed data into the tracula pipeline for just the path reconstruction and stats steps? I have already run recon-all too. Or perhaps is there a way I can insert my own corrected images into the prep step if it is running extra steps. My main reason for not wanting to start again from scratch is timing (I have 100 participants), but also that my preprocessing steps are slightly different. I use Eddy instead of Eddy_correct, and some of my participants needed individualised values for BET to work correctly. Any advice would be great, Nicole

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Fwd: OHBM Call for Nominations
by Douglas N Greve 25 Jan '18

25 Jan '18

-------- Forwarded Message -------- Subject: OHBM Call for Nominations Date: Thu, 25 Jan 2018 16:15:20 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Organization for Human Brain Mapping *call for nominations* <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Dear OHBM Member: Both history and experience teach us that strong leadership is very important to the success of any Society. OHBM is no exception as we continue our strategic growth. The OHBM Nominating Committee is *requesting your participation now in volunteering for or identifying leadership candidates for open seats on the OHBM Council.* Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. The term of service begins immediately after the Council meeting in June 2018, and each term is for three years. Please nominate yourself or make a nomination by completing the Call for Nominations Form <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> no later than *Monday, February 19th at 24.00H-US Central.* The Council is committed to supporting a diverse membership and strongly encourages nominations from each geographic region, women, minorities, and members of other underrepresented groups from individuals at various career stages. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Christian Grefkes, Secretary Shella Keilhotz, Secretary-Elect Tor Wager, Past Secretary Bernard Mazoyer, Chair Vince Calhoun, Chair-Elect Alan Evans, Past Chair Tonya White, Chair, Diversity & Gender Committee Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the OHBM Annual Meeting in Singpore. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. Councilors are not eligible for re-election for any Council position for three years after their term ends on Council. Those currently serving on Council are also not eligible. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. Current 2017-2018 OHBM Council <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. *Not Eligible Until 2021/2022* * Alan Evans, Chair Term Ending 2018 * Michel Thiebaut de Schotten, Treasurer Term Ending 2018 * Tor Wager, Secretary Term Ending 2018 * Michael Greicius, Program Chair Term Ending 2018 * JB Poline, Education Chair Term Ending 2018 *Not Eligible Until 2020/2021* * Karen Berman, Chair Term Ending 2017 * Jeannette Mumford, Treasurer Term Ending 2017 * Doug Greve, Secretary Term Ending 2017 * Jack Van Horn, Program Chair Term Ending 2017 * Niko Kriegeskorte, Education Chair Term Ending 2017 *Not Eligible Until 2019/2020* * Steve Smith, Chair Term Ending 2016 * Jia-Hong Gao, Treasurer Term Ending 2016 * Simon Eickhoff, Secretary Term Ending 2016 * Pedro Valdes Sosa, Program Chair Term Ending 2016 We look forward to your involvement in the identification and election of your Society’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Phone: 1 952-646-2029 · i <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>nfo(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>·humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. © 2017 Organization for Human Brain Mapping. All Rights Reserved. Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3545&conta…>

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Re: [Freesurfer] New hippocampal subfields
by Maksimovskiy, Arkadiy 25 Jan '18

25 Jan '18

Hi Eugeno, I am hitting the same error as described in this post, but using a Dev El Capitan version. Here is my error output: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1.sh SILVA053 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Thu Jan 25 17:26:21 EST 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_El_Capitan/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_El_Capitan/MCRv84//bin/maci64:/Applications/freesurfer_Dev_El_Capitan/MCRv84//sys/os/maci64: Invalid MEX-file '/tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Expected in: /usr/lib/libstdc++.6.0.9.dylib in /tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile Darwin arkadiysnewimac.mclean.harvard.edu 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Thu Jan 25 17:26:27 EST 2018 Wondering if you might have resolved this already? Thank you for all of your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] White Matter Edits: Removing White Matter from the WM Surface
by Maksimovskiy, Arkadiy 25 Jan '18

25 Jan '18

Hi Bruce, My apologies if this email is coming in duplicate- I think the previous one bounced- so resending. Thank you for following up on this. Attached are the unedited (brainmask.auto). the defaced orig.nofix, and edited brainmask (brainmask), as well as the surface files. Let me know if you need any other files. Also attached is a screenshot of the coordinates. Let me know if you need anything additional to diagnose. These was no orig.nofix file inside the transforms, but let me know if these are not enough to diagnose. This is a strange error to me as well. Thank you for all of your help with this! I really appreciate it. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School [cid:image001.png@01D395EA.DA1F0BF0]

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mri_em_register and mri_ca_register
by Ricardo Valle 24 Jan '18

24 Jan '18

Dear Freesurfer community, I would like to get a better sense of how mri_em_register and mri_ca_register work. I understand the former is a linear registration and the latter is nonlinear, and that they are both meant to register an individual to a template space (MNI152?). Would it be possible to update the wiki pages to give more information about the algorithms and cost functions used and other such details? And to provide references to the literature in support of the algorithms if possible? Thank you. Best regards, Ruy

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Does paracentral include precentral area
by Shatil, Anwar Shahadat 24 Jan '18

24 Jan '18

Hi Doug: I am confused about the visualisation of “Paracentral” and “precentral” clusters after running mri_glmfit-sim command. I used two cache values (3 pos and 4 pos) to see if the area changes. Each time the “Paracentral” cluster appears to be the largest significant area, but, the area shrinks during the cache value of 4 pos. It seems that paracentral and precentral areas are not mutually exclusive. I.e. paracentral seems to include precentral. Is that true? If not, then how can I visualize the actual significant area despite seeing a large “Paracentral” or “Precentral” area. Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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