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30132 discussions

Does data orientation (Neurological Vs. Radiological) produces different results
by Meena M. Makary 13 Dec '18

13 Dec '18

External Email - Use Caution Hi; I am wondering if the orientation of the input data to recon-all (i.e. Neurological Vs. Radiological) produces different results in terms of laterality (right vs. left)? Thanks; --Meena — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Yale University School of Medicine <http://people.yale.edu/search/meena_beshara.profile> Postdoctoral Associate | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Postdoc Committee Chair | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592 <+1%20475-731-5592>

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Re: [Freesurfer] How to use FIR to get HRF shape
by Lauri Tuominen 13 Dec '18

13 Dec '18

External Email - Use Caution I want to test if there is an increase in the HRF delay in a certain condition. I would like the time resolution to be higher so that the time to peak is measured as accurately as possible. I thought this would be the idea of not locking the events with the TR. Am I completely lost here? Cheers! Lauri Hi Lauri, what is non-ideal about it? doug On 12/06/2018 05:30 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Hi there, > > I would like to know if a condition leads to a delayed HRF peaking. > > To device an experiment to answer this, I collected finger tapping pilot data with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, TR=1.6. > > The trials are not TR locked because I thought I?d sample different portions of the HRF during each trial. > > I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. > > My problem is that the resulting ces.nii.gz has only 16 volumes, which correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time resolution for peak detection would be 1.6, which is not what I would like it to be. This is obviously less than ideal for answering my research question. > > How could I get the FIR fit to each timepoint so I could reconstruct the HRF myself? Or would there be some other workaround / analysis? Or do I need to collect the data in some other way, i.e somehow sliding the TR-event locking? > > Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, iminsig.nii.gz and minsig.nii.gz? > > Thanks so much again for the help > > Lauri Tuominen >

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Re: [Freesurfer] Recon command with T1 and T2
by Maksimovskiy, Arkadiy 13 Dec '18

13 Dec '18

Got it. Thank you!

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Re: [Freesurfer] Recon command with T1 and T2
by Maksimovskiy, Arkadiy 13 Dec '18

13 Dec '18

Hi Doug, I have a follow up question, if you don’t mind clarifying. My goal is to optimize the reconstruction and increase its accuracy. Would you mind confirming if the flag selection is appropriate for the following scenarios: Multiple T1 scans and one T2 scan: Use the 3T flag and the -T2pial flag (is combining them allowed?). One T1 scan and one T2 scan: Use only the -T2pial flag . I would love to hear if these are correct. Thank you for your help, arkadiy

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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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