Freesurfer

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Re: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH
by fsbuild 13 Dec '18

13 Dec '18

External Email - Use Caution Unless you turn off SIP, both DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH are always ignored now at run time (since Mac OS 10.11, El-Capitan).I don't think you should need to set those in order to run Freesurfer 6.0.0 release binaries on a Mac if you are in the Freesurfer shell (download link to 6.0.0 .dmg file, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Dar… recently built the latest development (dev) branch of Freesurfer on Mac OS 10.14 using the new cmake builld.  You can do this using homebrew on a Mac with the gcc 5 compiler package.  If you use the wrapper (makefile.wiki) from https://surfer.nmr.mgh.harvard.edu/fswiki/CMake, you can download and try to use the homebrew git project w/o having to install homebrew on your machine (and pollute /usr/local).  But please beware that the dev branch has not been tested like the previous 6.0.0 release.- R. On Dec 13, 2018, at 04:36, ts+ml(a)rcmd.org wrote:       External Email - Use Caution        Without the full command line and error message it is hard to tell, but this may be an issue with the System Integrity Protection of Mac OS. Try turning it off and see whether that helps.TimOn December 13, 2018 at 10:05 AM Jaime Gomez <borriquear(a)gmail.com> wrote:       External Email - Use Caution        Hi ,segmentHA_T1.sh of the dev version produces very often segmentationviolation errors.In the case I attach, it did the left hemisphere but when started theHippocampal Subfields processing (T1) right it terminates with SegmentationViolation Error.The computer where I'm running the script is a 16GBProductName:    Mac OS XProductVersion:    10.14.1BuildVersion:    18B75Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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segmentHA_T1 error DYLD_LIBRARY_PATH
by Jaime Gomez 13 Dec '18

13 Dec '18

External Email - Use Caution Hi, I have this error when I try to run segmentHA_T1.sh It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my bash_profile is /Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64: [~/val...V/003_SAG_3D_IR] $ segmentHA_T1.sh sujeto_uno #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Oct 30 12:04:16 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 7887 Abort trap: 6 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- --

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Power analysis
by Laura Ferrero 12 Dec '18

12 Dec '18

External Email - Use Caution Hi, I want to perform a power analysis and I read that I need 3 of 4 things: 1. Effect size (mean/std) 2. False positive rate 3. Number of subjects 4. True positive rate I also read that the effect size can be calculated using gamma.mgh and gammavar.mgh files but I do not know how to open them in order to get the numbers. Thank you, Laura

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Job ad: small animal MRI faculty position
by Keith Schneider 12 Dec '18

12 Dec '18

External Email - Use Caution Associate Professor, Behavioral Neuroscience University of Delaware: College of Arts & Sciences: Psychological & Brain Sciences Location: Newark, DE The University of Delaware invites applications for a tenured associate professor (or assistant professor nearing tenure) in behavioral neuroscience to begin September 1, 2019. We are seeking to hire a scholar with a solid background in small animal fMRI and/or DTI at ultrahigh fields for linking systems neuroscience and brain MR imaging (the university has a 9.4T/30cm Bruker MRI for animal research). The exact discipline area is open for this position as scholarly excellence will be the primary consideration. Ideal candidates will have extensive experience in brain science-oriented MR research, demonstrate outstanding and innovative scholarship, and have collaborative and synergistic possibilities with existing researchers at UD. The candidate should enjoy collaborating with researchers from various disciplines (e.g., medical engineering, biochemistry) and helping researchers new to MRI. This is an outstanding opportunity for a scholar to join and strengthen the growing Department of Psychological and Brain Sciences (https://www.psych.udel.edu <https://www.psych.udel.edu/>) and University of Delaware (https://www.udel.edu <https://www.udel.edu/>) that already has a promising core of interdisciplinary researchers utilizing cutting edge methodologies. An innovative leader in research and teaching, the University of Delaware combines a rich historic legacy with a commitment to education and the latest in advanced technology. With external funding exceeding $200 million per year, the University ranks among the top 100 universities in federal R&D support for science and engineering. Enhanced by state-of-the-art facilities, research is conducted across all seven colleges and numerous interdisciplinary institutes and centers. Relevant facilities on campus include the new 11,600 square foot Center for Biomedical and Brain Imaging, housing the 9.4T/30cm Bruker MRI, a 3T Siemens Magnetom Prisma, and transcranial magnetic stimulation machine; a 103,000 square foot Health Sciences Complex, a facility that includes labs for small animal and human-based studies, and an active outpatient clinic; a 194,000 square foot Interdisciplinary Science and Engineering Laboratory; and the Delaware Technology Park, where entrepreneurial and academic research labs are co-located. The Delaware Health Sciences Alliance (DHSA), a partnership among the University of Delaware, Christiana Care Health System <http://www.christianacare.org/>, Nemours/Alfred I. du Pont Hospital for Children <http://www.nemours.org/welcome.html>, and Thomas Jefferson University <http://www.tju.edu/>, provides infrastructure and opportunity for innovative clinical and translational collaborations. The University of Delaware is located in Newark, Delaware, which is only a short drive or train commute from Philadelphia, PA. UD is also within driving distance of New York City, Baltimore, Washington DC, the Poconos and some of the finest beaches in the country, making it an ideal location for day or weekend trips. QUALIFICATIONS Applicants for this position must have earned a Ph.D., tenure (or be nearing tenure), have a history of high-level publications in behavioral neuroscience or related fields, and conduct fundable research. APPLICATION INSTRUCTIONS Using the Interfolio system at UD, http://apply.interfolio.com/58701 <http://apply.interfolio.com/58701>, applicants submit a cover letter, a statement of research, a current curriculum vitae, three representative publications, and three confidential letters of reference. Inquiries, but not application materials, should be emailed to Jeffrey Rosen, Chair of the small animal MRI Faculty Search committee, jrosen(a)psych.udel.edu. Review of applications will begin on January 15, 2019 and will continue until the position is filled. The University of Delaware is an Equal Opportunity Employer which encourages applications from minority group members and women. The University's Notice of Non-Discrimination can be found at http://www.udel.edu/aboutus/legalnotices.html. ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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recon-all ERROR: killed
by 张亮军 12 Dec '18

12 Dec '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use "recon-all -i T1.nii.gz -s zhang -all", but there is a ERROR: saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt Killed Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s zhang exited with ERRORS at Wed Dec 12 22:18:35 CST 2018 For more details, see the log file /usr/local/freesurfer/subjects/zhang/scripts/recon-all.log I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu16.04 LTS(VMware Workstations pro) 3) uname -a: Linux ubuntu 4.10.0-37-generic #41~16.04.1-Ubuntu SMP Fri Oct 6 22:42:59 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: killed Best, Liangjun.

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Beta series method in FS?
by Hahn, Emily M. 12 Dec '18

12 Dec '18

Hi, I am interested in using the beta series method (https://neuroscape.ucsf.edu/wp-content/uploads/publications/Rissman2004-Mea…) for intra-subject analysis. Is there a straightforward way to do this in FreeSurfer? I attempted and the following analysis (code starting @ foreach) and an error appeared at the selxavg3-sess step: ERROR: condition ids are not contiguous Should I include a positive contrast for each condition (i.e. instead of '-no-con-ok', use 'mkcontrast-sess -analysis $analysis -contrast $contrast -a $1_to_194') or is something else about the design erroneous? Thank you in advance for feedback. Notes regarding the paradigm file: (1) treats each condition type as a unique event (i.e. second column consists of numbers 1:194; $Nconditions = 194) (2) stim weight == 1 (i.e. third column all ones) foreach cortices ( lh rh ) mkanalysis-sess \ -fsd $fsd \ -surface fsaverage $cortices \ -fwhm $FWHM \ -event-related \ -paradigm $paradigm \ -nconditions $Nconditions \ -spmhrf 0 \ -TR $TR \ -refeventdur $EVENT_DUR \ -nskip $Nskip \ -hpf $HPF \ -analysis bsm.analyses.$cortices \ -per-run \ -nuisreg $MC_nuis -1 \ -tpexclude $MCR_censor \ -force end foreach cortices ( lh rh ) selxavg3-sess \ -s $SUBJECT \ -analysis bsm.analyses.$cortices \ -no-con-ok end ------ Emily M. Hahn | Clinical-Computational Research Coordinator Division of Neurotherapeutics | A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School

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Download link for Matlab runtime broken?
by raul perez moraga 12 Dec '18

12 Dec '18

External Email - Use Caution Hello! I tried to download the Matlab runtime for Linux to use FSFAST but the link is broken. https://surfer.nmr.mgh.harvard.edu/pub/dist/mcr/MCRv83_linux.tar.gz Not Found The requested URL /pub/dist/mcr/MCRv83_linux.tar.gz was not found on this server. ------------------------------ Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443 Thanks in advance Raúl

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Problems with GM segmentation -- How to solve it
by Rosalia Dacosta Aguayo 12 Dec '18

12 Dec '18

External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull stripping, and using control points to improve white matter segmentation. Furthermore, the few participants I had problems with due to large ventricles were solved using the flag you recommended me to use. I am very grateful for all your help. However, I am facing another problem I thought I could solve using control points as well but this is worsening things instead of improving them. I refer to grey matter segmentation. I have found that several participants, more than I would like, are having problems with grey matter segmentation in the ventral temporal lobes and in the occipital lobe as well. I wonder if you could kindly help me with this, telling me how I could solve this problem so GM and WM segmentation are fine. Yours sincerely, Rosalia

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aparc regions misclassified
by Simon Jones 11 Dec '18

11 Dec '18

External Email - Use Caution Hi all, I have some participants whose recons look OK except the parcellations are incorrect. For instance the right precentral gyrus should be postcentral in three people. This appears as a shifting of multiple regions posteriorly. Is there a way to fix this? Thanks for your help, Simon

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Classification of amygdala subregions using Freesurfers new Algorithm
by Sally Grace 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Eugenio and experts, I have run the segmentation of the hippocampus subfields and nuclei of the amygdala using the latest algorithm implemented in the development version of Freesurfer. We have a priori hypotheses regarding the basolateral amygdala. I understand that you have broken the amygdala output down into the distinct subregions, e.g., the basal, lateral and accessory basal amygdala nuclei. Based on this reference https://www.physiology.org/doi/pdf/10.1152/physrev.00002.2003, my understanding is that the "basolateral nucleus" is comprised of the basal and lateral nucleus of the amygdala and the "basolateral nuclei" (aka. basolateral complex) comprises basal, lateral and accessory basal nuclei. So, I can create a variable called the "basolateral nucleus" (by adding together the basal + lateral) and the "basolateral complex" (by adding together basal + lateral + accessory basal). Is this assumption correct? Kind regards, Sally.

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