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FW: Postdoc position in neuroimaging-genomics studies
by Sennott, Liam Ricker 16 Jun '25

16 Jun '25

Posted on behalf of zhiq.sha(a)gmail.com<mailto:zhiq.sha@gmail.com> From: Z S <zhiq.sha(a)gmail.com> Date: Monday, June 16, 2025 at 10:11 AM To: freesurfer-owner(a)nmr.mgh.harvard.edu <freesurfer-owner(a)nmr.mgh.harvard.edu> Subject: Postdoc position in neuroimaging-genomics studies External Email - Use Caution Zhiqiang Sha's lab (https://shazhiqiang.wixsite.com/sha-lab<https://secure-web.cisco.com/1p-qub4e6wW7OPjQDli2Uf0lBCwFDQ_MqAxO2RDtQj5zbt…>) at the University of South Carolina is seeking an exceptional postdoctoral fellow to lead projects in neuroimaging-genomics/transcriptomics. This position focuses on investigating how genetic factors (e.g., genomics) and environmental factors (e.g., early life stress) influence brain development and neurodevelopmental disorders such as autism spectrum disorder. Research will integrate both in-house datasets and large-scale public resources. Our lab investigates the neurophysiological mechanisms underlying neurodevelopmental disorders by integrating multimodal biomedical data from both in-house and public datasets (e.g., UK Biobank, ABCD, HBCD, and etc.), including neuroimaging, genomics, and transcriptomics. These innovative projects will leverage state-of-the-art computational models and AI algorithms, supported by the brand-new Brain Imaging Center (with high-field 7T MRI) and the Biobehavioral Research Center. As a postdoctoral fellow, you will lead this interdisciplinary project and benefit from close mentorship and collaborative opportunities in a supportive and productive research environment. You will have full access to (1) rich in-house and public datasets; (2) advanced neuroimaging platforms (3T and 7T MRI); (3) biobehavioral and clinical research resources. You will conduct a range of neuroimaging and genomics-based analyses, design and implement computational models, and lead manuscript preparation. The role also includes: (1) collaborating with international research collaborators; (2) presenting work at international conferences and institutional seminars. What we offer: We assist postdoctoral researchers in applying for internal and external grants and provide structured mentorship tailored to each individual's career goals. Our lab fosters a collaborative and productive environment, and we actively support postdocs in building their academic networks, generating high-quality research publications, and securing independent faculty positions. Requirements: The ideal candidate will hold a Ph.D. in neuroscience, bioinformatics, biomedical sciences, psychology, or a related field. A strong interest in programming is essential (e.g., Python, R, Matlab, or Linux). The successful applicant will be highly motivated, possess strong analytical and problem-solving skills. Excellent communication skills and the ability to work both independently and collaboratively in an interdisciplinary research environment are also required. How to apply: submit your CV to Dr. Zhiqiang Sha (zsha(a)mailbox.sc.edu<mailto:zsha@mailbox.sc.edu>). We encourage applications from individuals of all backgrounds who are passionate about neuroscience.

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Re: Query related to controlling for ICV in the models for surface area and thickness
by Douglas N. Greve 14 Jun '25

14 Jun '25

I'm not sure what you mean. Can you elaborate? On 6/11/2025 5:09 PM, kingwai.chu(a)gmail.com wrote: > > External Email - Use Caution > > Hi Doug, > > What about the argument of using eTIV^(2/3) makes the scaling > dimensionless? > > Best, > > King-Wai > > *From:*Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Wednesday, June 11, 2025 4:09 PM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Re: Query related to controlling for ICV in > the models for surface area and thickness > > Yes, it is recommended. The exact form it should take is in dispute, > namely whether you should correct by the eTIV or the eTIV.^(2/3). The > second is motivated by the idea of a sphere whose surface area grows > with the 2/3 power of the volume. But cortex is not a sphere -- it is > folded, so the area can grow faster than 2/3 power. I usually just > scale by eTIV. When you run mris_preproc, you can add the --etiv > option and it will do the scaling for you. > > On 6/11/2025 4:05 AM, Muskan Khetan wrote: > > * External Email - Use Caution * > > Dear Team members, > > I have a question regarding vertex-wise analysis using FreeSurfer. > In my current analysis, I’m looking at the effects of an > independent variable on cortical thickness and surface area across > the brain. > > I understand that forROI-based surface area analyses, it is > typically recommended to control for total brain volume (TBV) or > intracranial volume (ICV), as surface area is correlated with > these global brain size measures. However, I’m unsure whether this > recommendation applies tovertex-wise analysesas well or whether > anyunderlying preprocessing stepsin FreeSurfer account for brain > size differences automatically. > > Could you please advise on whether TBV or ICV should be included > as covariates in vertex-wise surface area models? And more > broadly, under what circumstances is it advisable to control for > global brain size in vertex-wise analysis? > > Any insights would be greatly appreciated. > > Best, > > Muskan > > > > _______________________________________________ > > Freesurfer mailing list --freesurfer(a)nmr.mgh.harvard.edu > > To unsubscribe send an email tofreesurfer-leave(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.… <https://secure-web.cisco.com/1zgqCqj4qntd9bt8wznuUVVVTiFZuyVa-TmLzp-uKKBcf3…> >

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Re: any updates on installing on Ubuntu 24?
by fsbuild 12 Jun '25

12 Jun '25

External Email - Use Caution   Recent freesurfer releases list the supported OS’s on the web page,https://secure-web.cisco.com/14dxuu_DbHG9-OdhIKIO4mT7TZRdP453JQfldXjZ0… While Ubuntu24 is not listed for 8.0.0, it is on the list to support for future releases. Recent changes in Linux OS’s prevent binary backwards compatibility when upgrading to Rocky9, CentOS9, Ubuntu 24. - R. On Jun 12, 2025, at 13:59, William Graves <william.graves(a)rutgers.edu> wrote:        External Email - Use Caution        Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ...dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however:  Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however:  Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however:  Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfiguredProcessing triggers for libc-bin (2.39-0ubuntu8.4) ...Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best,Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ  07102 http://secure-web.cisco.com/1NPzbSguN782gCrsIkTAvR6KDkkdSIQ9Rze0CwYkPXW7LPQ… _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1V0E1aPavCVV45TGCyLOq0zPzHsNXPELJIyxY000FGU3PO…

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any updates on installing on Ubuntu 24?
by William Graves 12 Jun '25

12 Jun '25

External Email - Use Caution Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ... dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however: Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however: Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however: Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfigured Processing triggers for libc-bin (2.39-0ubuntu8.4) ... Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best, Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/10xSdrnQwPN0s0wFvnWgnpsjwfLF9AmsaUlcaB4xmPD1xZ5…

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Please stop copying me on these emails. I no longer require updates on this matter.
by Joseph 12 Jun '25

12 Jun '25

External Email - Use Caution Please stop copying me on these emails. I don't require updates on this matter.

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Computational Neuroscience Post Doc job opening
by Thomas Funck 12 Jun '25

12 Jun '25

External Email - Use Caution Hi everyone, We currently have a job opening for a Post Doctoral Fellow in computational neuroscience, specifically for neural mass modeling. The position is based in New York City and is for 3 years. Please see the attached pdf for job details. Feel free to reach out if you have any questions or want to discuss further! Cheers, Thomas Funck, PhD Research Scientist Child Mind Institute This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message and any attachments

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Re: any updates on installing on Ubuntu 24?
by fsbuild 12 Jun '25

12 Jun '25

External Email - Use Caution  Recent freesurfer releases list the supported OS’s on the web page,https://secure-web.cisco.com/1-84lS_-Js-6g7gOAWL8t--PWCh83WInKO14q7DSc… While Ubuntu24 is not listed for 8.0.0, it is on the list to support for future releases. Recent changes in Linux OS’s can prevent binary backwards compatibility when upgrading to Rocky9, CentOS9, Ubuntu 24. - R. On Jun 11, 2025, at 22:07, William Graves <william.graves(a)rutgers.edu> wrote:        External Email - Use Caution        Dear FreeSurfer experts, In searching your email list archive, I saw a message from Feb 5 of this year about known issues with installing FreeSurfer on Ubuntu 24. Any updates on whether those issues have been resolved? I ask because when I download and try to install the .deb package for freesurfer 8.0, I get this: Unpacking freesurfer (8.0.0) ...dpkg: dependency problems prevent configuration of freesurfer: freesurfer depends on libncurses5; however:  Package libncurses5 is not installed. freesurfer depends on libc6 (<< 2.36); however:  Version of libc6:amd64 on system is 2.39-0ubuntu8.4. freesurfer depends on libicu70 (>= 70.1-1~); however:  Package libicu70 is not installed. dpkg: error processing package freesurfer (--install): dependency problems - leaving unconfiguredProcessing triggers for libc-bin (2.39-0ubuntu8.4) ...Errors were encountered while processing: freesurfer I’d appreciate any insight you could give! Best,Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ  07102 http://secure-web.cisco.com/1cXCzSOEdcDFawBCD5-AuANnnfi-8MvW9k8OYOzjwZVMCeL… _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1vhVZTW4j8zk-aMIqGXiHh8iT6iUL5_5VaC_XGhTwDRfLw…

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Query related to controlling for ICV in the models for surface area and thickness
by Muskan Khetan 11 Jun '25

11 Jun '25

External Email - Use Caution Dear Team members, I have a question regarding vertex-wise analysis using FreeSurfer. In my current analysis, I’m looking at the effects of an independent variable on cortical thickness and surface area across the brain. I understand that for ROI-based surface area analyses, it is typically recommended to control for total brain volume (TBV) or intracranial volume (ICV), as surface area is correlated with these global brain size measures. However, I’m unsure whether this recommendation applies to vertex-wise analyses as well or whether any underlying preprocessing steps in FreeSurfer account for brain size differences automatically. Could you please advise on whether TBV or ICV should be included as covariates in vertex-wise surface area models? And more broadly, under what circumstances is it advisable to control for global brain size in vertex-wise analysis? Any insights would be greatly appreciated. Best, Muskan

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any updates on installing on Ubuntu 24?
by William Graves 11 Jun '25

11 Jun '25

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Question Regarding Longitudinal vs. Cross-Sectional FreeSurfer Analysis
by Keller, Lara 11 Jun '25

11 Jun '25

External Email - Use Caution Dear FreeSurfer Community, I am currently analyzing structural MRI data using FreeSurfer 8 and have a specific question regarding the longitudinal pipeline. My dataset consists of two groups: * One group has 3 follow-up timepoints * The other group has 2 follow-up timepoints I have processed the data using both the cross-sectional and longitudinal recon-all pipelines, and I am now wondering whether it is appropriate to proceed with the longitudinal output, despite the unequal number of timepoints between groups. Key Concerns: 1. Since FreeSurfer creates subject-specific within-subject templates, could the differing number of sessions lead to relevant systematic differences between the groups? Specifically, will the segmentation accuracy or signal-to-noise ratio be noticeably different between the groups due to these variations? 2. Would it be valid to continue using the longitudinal output but statistically account for the unequal number of sessions (e.g., via Linear Mixed Models)? 3. Alternatively, would it be preferable to use cross-sectional outputs to avoid potential biases introduced by differing template quality? 4. If I analyze only one specific timepoint for certain research questions, should I still use the longitudinal output, or would cross-sectional data be more appropriate? I find myself torn between the improved segmentation accuracy of the longitudinal approach and the potential systematic differences introduced by the varying number of timepoints. Would a viable solution be to proceed with the longitudinal output while ensuring robustness by replicating key findings using cross-sectional data? I would greatly appreciate your insights on whether it is methodologically sound to proceed with the longitudinal pipeline in this case and, if so, how best to control for the unequal timepoints in statistical analysis. Thank you very much for your time and guidance! Best regards, Lara

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