Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Postdoctoral Positions in Language Neurobiology at the University of Texas at Houston (UO1/RO1 funded)
by Klier, Eliana M 17 Nov '18

17 Nov '18

External Email - Use Caution POSTDOCTORAL RESEARCH POSITIONS IN THE NEUROBIOLOGY OF LANGUAGE AT THE UNIVERSITY OF TEXAS AT HOUSTON Multiple Postdoctoral research positions are available in the Tandon Lab at The University of Texas in Houston as part of the newly formed Texas Epilepsy Neurotechnologies and Neuroinformatics (TENN) Institute. Positions are funded either via multi-year Institute funding or by NIH funds (U01 and R01). The lab uses multimodal approaches - fMRI, lesional analysis following epilepsy surgery, intracranial recordings and direct stimulation to create and validate network level representations of language. Lab Collaborators include Greg Hickok (UCI), Stanislas Dehaene (NeuroSpin), Nathan Crone (JHU), Simon Fisher Baum (Rice) and Xaq Pitkow (Rice-Baylor); the post-doc will benefit from a close interaction with these experts in the fields of reading, semantics, speech production and computational neuroscience. The selected individual must have a Ph.D. in one or more of the following: neuroscience, psychology, cognitive science, mathematics, electrical engineering or computer science. Previous experience in neural time series data analysis, functional imaging studies of language, or studies of speech production are desirable - but not crucial. They must possess the ability to independently code in any or all of the following: MATLAB, R or Python. They are expected to be highly motivated, team players with a passion to study cognitive processes using any or all of the various modalities available in the lab - imaging, direct recordings and closed-loop cortical stimulation - in humans. Given the multiple unpredictable variables and privacy issues around data collection in human patients, the individual must possess high ethical and professional standards and be adaptable. A strong publication record and excellent academic credentials are highly desirable. CONTACT: Nitin.Tandon(a)uth.tmc.edu Eliana.Klier(a)uth.tmc.edu More information @ www.tandonlab.org

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回复： ?????? Recon-all run error
by 1013364183 16 Nov '18

16 Nov '18

External Email - Use Caution Dear Bruce Fischl, I am very sorry that I have not reply to you last week. Our data has been running for a few weeks, but the computer did not react. There is a log file in the attachment. We want to ask that could you help us run the data? We will send you a set of data firstly(We still have two sets of data). If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person. The download link is: https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=… https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=… Looking forward to your reply. Thanks in advance yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Computation time
by Dawn Matthews 16 Nov '18

16 Nov '18

External Email - Use Caution Dear Freesurfer team, Thank you for your continued efforts and advances on the Freesurfer tool, which have benefitted the community and quest for therapy advances. I wondered whether there is an assessment of the computation time breakout between volume calculation vs. cortical thickness, area, and mean curvature. Is it possible to reduce time by calculating only volumes (no CT, area, MC), and if so, what reduction would be anticipated (recognizing that the answer is proportional as the absolute time would depend upon hardware etc.)? As a second question, there was a previous mention in listserv comments regarding running left and right hemispheres in parallel. Is this done, and is it an approach that can be combined with the parallel processing flag? Thank you for any insights on these questions. Dawn

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Scripts to prepare MP2RAGE sequence for recon-all pipeline
by Marcel Heers 16 Nov '18

16 Nov '18

External Email - Use Caution Dear all, does anyone share scripts to prepare MP2RAGE sequences for freesurfer's standard processing pipeline, e.g. the method used by Fuijmoto et al. NeuroImage 2014? Thanks for your help! Marcel

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Minnesota Center for Twin and Family Research (MCTFR) Post-Doctoral Associate Position
by Sylia Wilson 16 Nov '18

16 Nov '18

External Email - Use Caution The Minnesota Center for Twin and Family Research (MCTFR) seeks to hire a “Post-Doctoral Associate” (9742R5: Researcher 5) interested in identifying deviations in brain structure and white matter organization associated with problematic alcohol use. As part of a two-year project funded by the National Institute on Alcoholism and Alcohol Abuse (PI: Dr. Sylia Wilson), the postdoctoral associate will be primarily responsible for processing and analyzing anatomical and diffusion weighted imaging data already collected in multiple large, adult samples, including a sample of twins from the MCTFR (N = 1152) and a sample of twins and their nontwin siblings from the Human Connectome Project (N = 1113). The postdoctoral associate will take the lead on and contribute to manuscripts developing from this project. In addition to the primary project, the MCTFR has several ongoing, large-scale, NIH-funded projects (PIs: Drs. William Iacono, Matt McGue, Monica Luciana, Scott Vrieze) examining biological and environmental contributors to the development of substance misuse and related psychopathology. Comprehensive, multimodal (clinical, personality, neurocognitive, psychophysiological, imaging) data have been collected at multiple time points in twin and adoption samples prospectively assessed from preadolescence into middle adulthood. The postdoctoral associate will have ample opportunities to work with and prepare manuscripts using existing data from these projects. Candidate expectations are: (1) Ph.D. in psychology, neuroscience or related field; (2) neuroimaging experience; and (3) expertise as demonstrated through publications or funded research. The applicant will join an interdisciplinary team of researchers (including neuroscientists, geneticists, psychopathologists, developmental psychologists, and statisticians) interested in the development of substance use and other common mental disorders. The MCTFR dataset is unique in terms of the breadth of its assessment (e.g., a rich set of clinical, personality, and endophenotypic measures), developmental informativeness (participants have been assessed every 3-4 years, spanning ages 11 through 42), comprehensive measurement of environmental risk (e.g., prenatal, familial, peer group, neighborhood), inclusion of biological measures (e.g., anatomical, resting state, functional MRI; DTI; dense array EEG/ERP; neuropsychological function) and extensive coverage of molecular genetic variants in prospectively studied samples of twins and twins’ parents and children (1800 pairs). The MCTFR affords excellent opportunities for the person filling this position to develop an independent program of research in addition to working with these data. Major Responsibilities • (10%) Collaborate with MCTFR principal investigators, research associates, other post-doctoral associates, graduate students, and undergraduate students to develop and advance research topics; • (20%) Process and analyze MRI data relevant to brain structure and function; • (40%) Develop and complete hypothesis driven research focusing on MRI data and relating it to other MCTFR data predicting, mediating, and moderating variables in composite datasets using epidemiological, behavior genetic, longitudinal and other data analysis methods; • (10%) Prepare preliminary reports for MCTFR Principal Investigators and our research seminar; • (20%) Publish at least four papers annually in top research journals. Essential Qualifications • Ph.D. in psychology, neuroscience or related field; • One or more years of graduate school research training; • Strong publication track record in top research journals. Preferred Qualifications • Neuroimaging processing and analysis experience; • Prior experience preparing proposals for sponsored research funding; • Skills using standard imaging software (e.g. FreeSurfer. FSL) and programming (e.g. MATLAB, R Python); • Excellent oral and written communication skills; • Additional experience and/or interest in cognitive/affective neuroscience, substance use and related psychopathology, and twin studies and behavior genetics methods is a plus. Required Application Materials (Application attachments) • An updated CV; • Personal statement; • Up to three reprints/preprints; • Contact information for three professional references. MCTFR The Minnesota Center for Twin and Family Research (MCTFR) seeks to identify environmental and genetic influences on psychological traits. The MCTFR includes studies of twins, adoptees, and biologically related adolescent siblings. MCTFR participants are involved in a variety of NIH-funded projects that include assessment of psychopathology, psychophysiology, neurocognitive, and MRI data, as well as collection of DNA samples. In addition to multiple large-scale projects with twins and twins’ parents and children, the MCTFR is now the twin research hub for the NIH Adolescent Brain and Cognitive Development (ABCD) project ( http://www.nih.gov/news-events/news-releases/nih-launches-landmark-study-su…) This position offers the opportunity to work in a high-quality research environment with strong scientific collaborations in the MCTFR, the Department of Psychology, and other departments (Institute of Child Development, Psychiatry), as well as the Center for Magnetic Resonance Research (CMRR). Appointment MCTFR Post-Doctoral Associate is appointed by the MCTFR’s Principal Investigators and reports to them. Position is 100%-time and classified as an academic professional appointment. It is contingent upon the availability of funds and/or work for the position. Appointment-provided health, dental, vacation and sick-time benefits plus is covered by Social Security and Faculty Retirement System. Position requires a background check and applicant must verify authorization to work in United States. Initial appointment is for one year but is renewable with acceptable performance. Salary is competitive and commensurate with education and experience. Interested applicants should send application materials by e-mail to Dr. Sylia Wilson at syliaw(a)umn.edu. Inquiries about the position can also be directed to Dr. Wilson. Review of applications will begin immediately and continue until the position is filled.

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glibc error: newly formatted license file?
by Juranek, Jenifer 16 Nov '18

16 Nov '18

External Email - Use Caution Recently our cluster underwent a major upgrade...which broke my well-established Freesurfer v 6.0.0 recon-all pipeline. 1) Error message from recon-all: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from <FSID>/mri/rawavg.mgz... -------------------------------------------------------------------------- GNU libc version: 2.22 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html 2) My attempt to download a "newly formatted" license file with this link results in what appears to be an identically-formatted license file (relative to my original one) 3) Is there a different process for obtaining a "newly formatted" license file? 4) Do I need to re-install Freesurfer v6.0.0? Many Thanks, JJ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Director of the BRAIN Lab Associate Professor Department of Pediatrics McGovern Medical School UTHealth Houston, TX 77030 713.500.8233

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Poor contrast between grey and white matter
by Borges Pereira Ines Isabel 16 Nov '18

16 Nov '18

External Email - Use Caution Dear FreeSurfer developers, For technical reasons regarding the MRI scanner used, the contrast between grey and white matter on the right hemisphere of a few of my subjects is very different from the contrast on the left hemisphere. This leads FreeSurfer to erroneously estimate the white matter (and subsequently pial) boundary (see attached image). To attempt to solve this issue, I am thinking of using the Livewire voxel draw on Freeview to manually obtain the white and grey matter boundaries. However, I was wondering what you would advise in such a situation, and if it is possible to solve this issue not having to rely on a 100% manual intervention. I am using the following Freesurfer version on Centos: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks! Best regards, Inês Pereira [cid:FFF896C0-6534-46C7-91FB-09A50BF2EF8D@ethz.ch]

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回复： ?????? Recon-all run error
by 1013364183 16 Nov '18

16 Nov '18

External Email - Use Caution Dear BrucenFischl, Our high resolution data has been running for a few weeks, but the computer did not react. It runs too slowly. We give our run commands and expert files as well as log files in the attachment. Please help us check if there is an error? If there are no errors, then can I use multithread in recon-all to speed up? Please give us some guidance. In addition, Could you help us run these data? We will send you 3 sets of data. We will give 9 download links because of these data is too large. If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person. The download link is: https://drive.google.com/file/d/1d8QMcSXjCq46HkqKFU-krpGTJO41eYbe/view?usp=… https://drive.google.com/file/d/1JHDmrVAHmzSO7NTZ0DsKmMwKh3HtDeyZ/view?usp=… https://drive.google.com/file/d/1ipC4svGbud_gvYEt9qF4oy3IGwmZhUuW/view?usp=… https://drive.google.com/file/d/1mKzYM2uNJEZv06nlP65sbBxa7S1gAwYh/view?usp=… https://drive.google.com/file/d/108y0FsujcaqDvQO7sYXcCTy9-gCoTzsD/view?usp=… https://drive.google.com/file/d/1NikZZDY0TPGXLjDdzgYayuOVh4BUl43g/view?usp=… https://drive.google.com/file/d/15da1mixza-1oH9uB1DXPKw5FluiuOmVe/view?usp=… https://drive.google.com/file/d/15W2MSnk5WUiToQBWRJS6VyCyMcQBFuK/view?usp=d… https://drive.google.com/file/d/1gVYV_UynTXKaWaAbYvreoY1O9574zU8s/view?usp=… Looking forward to your reply. Thanks in advance ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_glmfit-sim error
by C.P.E. Rollins 16 Nov '18

16 Nov '18

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt SURFACE: fsaverage lh log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log cd /home/cper2/BeneMin/Freesurfer /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Fri Nov 16 09:38:40 GMT 2018 Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux cper2 setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0 Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 26.134985 CSD /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh --sum lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary --ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh --no-fixmni --csd /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd --csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh --vwsigmax lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat --oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = lh srcid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 2 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh MGH ocnid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH sumfile = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary subjectsdir = /home/cper2/BeneMin/Freesurfer FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(?????): could not open file No such file or directory ---------------------------------------------------- Reading source surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white mri_surfcluster.bin: could not read surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white No such file or directory However, the files /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist and I can read them looking at the permissions. I was wondering if you might have any advice for this. Many thanks, Colleen

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Problems with skull stripping
by Rosalia Dacosta Aguayo 15 Nov '18

15 Nov '18

External Email - Use Caution Dear Free Surfer team, Sorry for double posting but I would like to explain well so it will be easier to understand what I am looking for. 1. I have run recon-all -all in a participant 2. The skull stripped image has skull and dura behind. 3. I can manual edit or I can do -autorecon1 and then supply the brainmask.nii.gz generated from my betted image. 4. Questions: a) If I run -autorecon1 and make the substitution of the brainmask: I am afraid this is not going to improve the grey matter and white matter segmentation. So, if this first step is not well solved, I think that then, no matter if I change my brainmask for a better one, that I will have the same problems with -autorecon2 and -autorecon3, is that correct? b) If I do manual edition, then I will have to run -autorecon1 again...not sure if this would be the best solution. As I am new to this, I would greatly appreciate your experience. Best wishes, Rosalia

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