Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

Pass code for freesurfer virtual images and QDEC question
by mariangela asimina 09 Apr '23

09 Apr '23

External Email - Use Caution Dear freesurfer team, I have been asked to re-run my analysis with QDEC, so I need to install a previous version in another computer(windows) using virtual box. Could you please give me the pass code for the archive? Alternatively, is it possible to run QDEC with the freesurfer 7+ versions? Or is it possible to have two different freesurfer versions on the same computer? Thank you! Mariangela Asimina

2 1

mris_flatten Version 6 vs. 7
by Nasr, Shahin,Ph.D. 08 Apr '23

08 Apr '23

External Email - Use Caution Hi Surfers, This is the second time that I have brought this issue up. When applied to the same 3D patch, the command mris_flatten generates two completely different outcomes when runs under stable 6 vs. 711 (see the attached files). I checked the documentation if there is any flags by which I can control the process. But I couldn't find anything relevant. Any idea what has happened? Regards Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzc…

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Fwd: Research scientist positions at OSUMC!
by Douglas N. Greve 07 Apr '23

07 Apr '23

Forwarding on an interesting job working Jessica Turner! -------- Forwarded Message -------- Subject: Research scientist positions at OSUMC! Date: Fri, 7 Apr 2023 13:42:55 +0000 From: Turner, Jessica <Jessica.Turner(a)osumc.edu> To: Douglas N. Greve <dgreve(a)mgh.harvard.edu> External Email - Use Caution https://osu.wd1.myworkdayjobs.com/OSUCareers/job/Medical-Center-Campus/Seni… <https://secure-web.cisco.com/1AFF-7GXWrl4IqEbcxoT3m-b8RLDQWdZfnUkXytxDqmooH…> _Job Description_ The Senior Researcher designs and conducts independent complex experimental research in a foundational (basic) biological/health science research laboratory with a psychiatric neuroimaging and genetics research program, in the Department of Psychiatry and Behavioral Health. Expected responsibilities include developing and investigating neuroimaging models of symptoms and response to various treatments across diagnostic groups; applying current analysis techniques to the analysis of behavioral, neurophysiological, and genetic data in combinations; interpreting and evaluating research data; working with collaborative multi-site teams in the analysis of large-scale data collections; preparing manuscripts, articles, reports and abstracts for publication in peer-reviewed journals; attending and presenting results at national and international scientific conferences, seminars, and workshops; collaboratively developing and contributing to grant proposals to obtain extramural funding to support research; developing and implementing new research projects; directing and training other research staff, participating in laboratory meetings and project meetings. Some mentoring of other research personnel may be available. _Minimum Education Required _ Doctorate (Academic) in psychology, biology, engineering, computer science, or a relevant field. _Required Qualifications _ The candidate will be analyzing data as part of their research work and must be capable of independently using some neuroimaging analysis pipelines (for example, fmriprep, SPM, FSL), ideally for structural, resting state, task-based analyses (the more imaging modalities the candidate has worked with, the better). The ability to work in a Linux environment is a must. Experience with multivariate analyses of functional MRI data or combined analysis of imaging and other datatypes such as EEG, EMA, PET, genetics is a strength. An interest in the integration of genetic data with neuroimaging and behavioral data within clinical populations is ideal. Clinical experience is not required but would be a strength. The candidate will also be writing in support of the research program, and must be capable of developing first author papers on neuroimaging results (as demonstrated by previous publications). Many thanks! Jess Jessica A. Turner, Ph.D. /Professor, Department of Psychiatry and Behavioral Health/ /Wexner Medical Center/ /The Ohio State University/ /jessica.turner(a)osumc.edu/

1 0

VM Password
by Janssen, J.A.M. (Julia) 07 Apr '23

07 Apr '23

External Email - Use Caution Dear Freesurfer developers, I am attempting to set up virtual box with the Ubuntu image provided in the installation guide. I would like to request the password to unzip 'FS_7_2_0_ubuntu_18_04_06.ova.7z' - I hope this is the right place to ask. If anyone knows it, would they kindly contact me? Thank you in advance!

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FreeSurfer container recipe?
by Bennet Fauber 06 Apr '23

06 Apr '23

External Email - Use Caution In reply to mail from Mitchell Horn, Douglas Greve replied > The math libraries changed between 7 and 8, nothing we can do about it. When I > have to run things on a centos8 machine, I generally run in a centos7 singularity > container (which we might be able to make available, without support:) Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki? We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too.. Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.

2 2

-gcareg dropped from -autorecon2-volonly
by Christopher Markiewicz 06 Apr '23

06 Apr '23

External Email - Use Caution Hi all, This is a duplicate of a bug report on GitHub (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY1…) `DoGCAReg` was removed from `-autorecon2-volonly` in commit 4b9af5fc8c559e944400b885ef89f3682f94e0da, but this seems unrelated to the commit message. It's still in `-autorecon2`. Is there a reason it shouldn't be present, or was this a mistake? This issue affects versions 7.3.0+. Apologies for doubling up if you saw it; my impression is the mailing list is more actively monitored. Best, Chris

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Open research assistant position at Ohio State University
by Osher, David E. 06 Apr '23

06 Apr '23

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience (every one of our research assistants has successfully been admitted into doctoral programs!). We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://secure-web.cisco.com/1TciY0h9Hnogs0Vsz6IpkMg3S9JvHoraefFGDv9JWfB8mv… and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://secure-web.cisco.com/1-CVKBQsgAyt6sw0qCo0o_YrQ6nEs-h_DI1v27Nd4YqU30…>

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some issues of -inflate operation
by 韦亚辉 06 Apr '23

06 Apr '23

External Email - Use Caution On Tues, 4 April 2023, YaHui Wei wrote:Hello freesurfers, I am getting some problems in pial reconstruction that the pial can not expand well to the real surface (result is below). Thus I’ve tried to check the ?h.inflated and ?h.inflated.nofix and found they had a large offset from the volume. The image below shows the volume, ?h.smoothwm and ?h.inflated. I wonder if the offset causing the pial reconstruction error, and if so how can I solve this problem. Can I get your suggestions? Thanks.

2 1

mri_glmfit correction across lobes
by John Anderson 06 Apr '23

06 Apr '23

External Email - Use Caution Hello Freesurfer, Currently, I am using the Petsurfer manual, which is easily understandable and clear. Nonetheless, I have a question regarding the "mri_glmfit" step. As far as I know, this command is used to correct data for multiple comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please confirm if my understanding is correct? mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir lh.patinets_vs_controls In particular, I am interested in correcting data across lobes instead of across all ROIs. I followed the steps mentioned in the FS forum to create lobes, and I can observe lobe annotations in the wmparc.mgz file. I am curious to know whether using the "--annot" flag will adjust the p-values across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file. I have attempted this, but it appears to only change the name of the annotation in the final statistics file, and the p-value remains the same. Do I need to include any additional arguments in the command? Thanks for your help John

2 3

lh.inflated and rh.inflated generated by mris_inflate is biased
by 韦亚辉 05 Apr '23

05 Apr '23

External Email - Use Caution On Tues, 6 April 2023, YaHui Wei wrote:Hello freesurfers, I found the ?h.inflated and ?h.inflated.nofix and found they had a large offset from the volume. The image below shows the volume, ?h.smoothwm and ?h.inflated. How can I solve this problem. Can I get your suggestions? Thanks.

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Freesurfer April 2023