Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

Re: [Freesurfer] can´t open an image in Freeview
by fsbuild 19 Oct '19

19 Oct '19

External Email - Use Caution Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam Rytina October 18, 2019 at 14:31         External Email - Use Caution         Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam Bez virů. www.avast.com _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Specialist Position on the MIDUS Neuroscience project's longitudinal study of aging, emotion, and well-being at the Center for Healthy Minds
by CHM Recruiting 18 Oct '19

18 Oct '19

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist. The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening, and scheduling for research at the University of Wisconsin-Madison's Center for Healthy Minds. This individual may work on several research projects examining the import of individual differences in the time course of emotional responses for varied domains including cognition, health, and well-being, while elucidating the critical functional and structural brain substrates underlying these relationships. One example of such a research project is the Neuroscience Project of the Midlife in the U.S. longitudinal study of health and well-being (http://midus.wisc.edu/) Please use the following link to see a full posting of the position and to apply online https://jobs.hr.wisc.edu/en-us/job/503196/research-specialist

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can´t open an image in Freeview
by Adam Rytina 18 Oct '19

18 Oct '19

External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Bez virů. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…>

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Post-doc on multi-tracer PET-MRI
by Linnman, Clas,Ph.D. 18 Oct '19

18 Oct '19

Hi everyone, My lab is looking for a post-doc. Please spread the below advertisement far and wide With my best regards Clas Linnman The Spaulding Neuroimaging Laboratory (PI Clas Linnman, assistant professor, Harvard Medical School), working closely with the Martinos Center for Biomedical Imaging, uses simultaneous PET-MRI with a focus on neuroinflammation and opioid receptors in humans and in animal models of chronic pain. The current position is part of a research project funded by the NIH to determine if intensive aerobic exercise may reduce inflammation, strengthen endogenous pain capacity, and improve rehabilitation outcomes in patients with spinal cord injury. Key Responsibilities Conduct neuroimaging research with emphasis on brain structure, network reorganization, opioid receptor expression and neuroinflammation after spinal cord injury. Evaluate the effects of intensive whole-body aerobic exercise in patients with sub-acute spinal cord injury with regards to pain inhibition capacity, spinal cord atrophy, brain function, opioid and neuroinflammation. Apply and develop MR and PET acquisition methods for longitudinal analyses Apply and develop research methodologies for integrating PET and MR data in human and animal models. Lead and assist in the writing of academic manuscripts Lead and assist in dissemination of research findings through presentations at conferences and for patient and public engagement activities. Initiate and assist grant applications for further career development Assist in mentoring of research assistants Qualifications Qualifications and Experience Education/Degree Required - A PhD degree in a field encompassing neuroscience and neuroimaging. Experience Preferred Research experience in neuroscience and neuroimaging; preferably in the fields of pain, SCI and MR data analysis, as demonstrated by at least one first-author publication for which MRI or PET methodology has been used. Candidates are expected to have considerable experience in the analysis of neuroimaging data, basic programming skills in Python or Matlab, and a solid understanding of inferential statistics. Excellent organizational, oral, and written communication skills Strong interpersonal skills and comfort interacting with research participants with spinal cord injuries English language fluency Excellent ability to work independently Familiarity with neuroimaging tools like Freesurfer, SPM, FSL Excellent attention to detail Apply online at https://partners.taleo.net/careersection/srn/jobdetail.ftl?job=3108990&tz=G…

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Research Specialist Position at the Center for Healthy Minds
by CHM Recruiting 18 Oct '19

18 Oct '19

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist! To learn more about this excellent job opportunity, please view the attached Position Description. Thank you, Center for Healthy Minds

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Group effect Contrast for 6 groups
by cody samth 18 Oct '19

18 Oct '19

External Email - Use Caution Hi, I'm designing an analysis that will have 6 groups (two factors/three levels). I was wondering if I could get some input regarding my contrast for the group effect. Based on the group effect contrast under the FSGD examples for 3 groups I've written a five line contrast file that compares group 1 against the other 5 groups. 1-1 0 0 0 0 1 0 -1 0 0 0 1 0 0 -1 0 0 1 0 0 0 -1 0 1 0 0 0 0 -1 Which from my understanding should cover the rest of the contrasts such as 2v5 3v6 and etc. Is my understanding of this correct?

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Mri_mask producing only zeros
by Sims, Sara A (Campus) 18 Oct '19

18 Oct '19

External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Sara A. Sims

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-multistrip exited with errors troubleshooting
by Mohn, Johannes 18 Oct '19

18 Oct '19

External Email - Use Caution Hi all, I'm trying -multistrip to improve skull stripping for subjects where incomplete skull strip lead to inaccurate pial surfaces. The command I'm running is: recon-all -multistrip -clean-bm -s <subjID> -no-isrunning However, multistrip fails. It exits with errors and no new brainmask.mgz files are created. This is independent of the subject. It fails for all. I attached the recon-all.log for one exemplary subject. In contrast, using -gcut (recon-all -skullstrip -clean-bm -gcut -s <subjID>) works but does not remove the problematic skull fragments in most cases. Independent of whether -multistrip or -gcut are better suited to improve the skull stripping, I would like to understand why -multistrip fails in my case and what can be done to make it work. Best, JJ

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brain mask without CSF ...
by stefano.silvoni＠libero.it 18 Oct '19

18 Oct '19

External Email - Use Caution Dear FreeSurfer Experts, I am running a functional analysis of subcortical structures using FS-FAST (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a brain mask excluding CSF; would it be possible using some option/flag in 'preproc-sess'? or should I do it manually? maybe using a command like that? mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o $sbjdir/mri/GM-WM_mask.mgz because I saw in FreeSurferColorLUT.txt the following definitions: 702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0 or is there another strategy? thanks in advance best stefano silvoni

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covariate with repeated anova
by miracle ozzoude 18 Oct '19

18 Oct '19

External Email - Use Caution Hello Experts, I would like to include covariates in the freesurfer repeated anova steps https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i tried including 3 covariates, mri_glmfit complained about "martix is ill-conditioned". How do i fix it? Below is an example my fsgd file. I've also attached the matrix design in the email. GroupDescriptorFile 1 Class PsyDis1 Class PsyDis2 Variables TP1vsTP2 Age Llesion Rlesion Input Psy1_Pre.long.Psy1 PsyDis1 1 68 96 61 Input Psy1_6mos.long.Psy1 PsyDis1 -1 68 96 61 Input Psy2_Pre.long.Psy2 PsyDis2 1 39 217 140 Input Psy2_6mos.long.Psy2 PsyDis2 -1 39 217 140 contrast: 0 0 1 0 0 Best, Paul

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Freesurfer October 2019