Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

TRACULA - custom tracts and path labelling
by Liliana Wu 18 Aug '22

18 Aug '22

External Email - Use Caution Hi, I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF) but I am seeing that this tract is not included in TRACULA. Does TRACULA enable manually selecting seed and target ROIs ? Also, I am trying to access the list of the abbreviated names for 42 pathways but I don’t seem to find it. I have tried looking at $FREESURFER_HOME/trctrain/hcp/pathlist.txt. as suggested per tutorial. I am new to TRACULA and I appreciate any help, Thank you, Liliana

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Neuroimaging Data Engineer position at University of Pennsylvania
by Jeff Phillips 18 Aug '22

18 Aug '22

External Email - Use Caution The Frontotemporal Degeneration Center (FTDC; https://secure-web.cisco.com/1hStz2eH3jXe2_6SYQbWkdC4nCQBiJDXOrnEBPo72L63UY…) at the University of Pennsylvania in Philadelphia, PA is looking for a neuroimaging data engineer to work on processing and analysis of multimodal MRI and PET data from our longitudinal neurodegenerative disease cohort. This is a great opportunity for an individual with imaging experience who wants to do unique imaging research as a staff scientist. Primary responsibilities include processing, analyzing and archiving neuroimaging datasets and facilitating integration of neuroimaging and clinical data repositories using the Integrated Neurodegenerative Disease Database (INDD) and cloud-based commercial platform FlyWheel. Neuroimaging datasets will include magnetic resonance imaging (MRI) and positron emission tomography (PET) series. The candidate will both implement existing pipelines and help develop novel pipelines. An additional primary responsibility will involve the training and co-supervision of neuroimaging analyses and general computing skills of junior lab personnel, including coordinators and research specialists. The candidate will also manage, receive, send, review, organize, process, and harmonize secondary data acquired via external collaborations and/or from publicly available data repositories, such as the Alzheimer’s Disease Neuroimaging Initiative. A third responsibility will be to perform basic statistical and bioinformatics analyses of imaging data to support the research of senior ADRC and FTDC staff and faculty. There will be publication opportunities for mentored research projects. Minimum qualifications include a bachelor's degree and two years of data analyst experience or an equivalent combination of education and experience. Required knowledge includes process and data modeling, data architectural development methodology and working knowledge of databases. Experience using data analysis tool and databases. Demonstrated competence in systems analysis and design and the ability to quickly learn and apply new technologies. Preferred qualifications include a master’s degree or PhD, plus 3-5 years’ experience in a computational (e.g., Computer Science, Bioinformatics) or biological (e.g., Biology, Neuroscience, Genomics) field or equivalent experience. Experience required with neuroimaging software (ANTs, FreeSurfer, SPM), programming/scripting (PERL, Python), open-source software development (Github), and working statistical knowledge (R, STATA, SPSS). Familiarity with neurodegenerative disease and/or psychiatric disorders is a plus. Must possess good organizational and time management skills, good written and verbal communications skills; ability to work independently and supervise others; be able to multi-task. Willingness to learn and keep current with technology and the rules and regulations involving clinical research a must. This position is continent upon grant funding. The FTDC enjoys close collaborations with the broader Penn neurology and neuroscience community, including the Alzheimer's Disease Research Center (ADRC), Center for Neurodegenerative Disease Research, Center for Cognitive Neuroscience, and Institute on Aging. For more details and to apply, please visit: https://secure-web.cisco.com/1OVx8sXmfwGjbGatlnZFYBlPhguVk1gBfDdFupynpMWI3f… Informal inquiries may be directed to Dr. Corey McMillan ( cmcmilla(a)pennmedicine.upenn.edu) or Dr. Jeff Phillips ( jefphi(a)pennmedicine.upenn.edu) Jeff Phillips Research Assistant Professor of Neurology Penn Frontotemporal Degeneration Center University of Pennsylvania Philadelphia, PA

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samseg lesions labels and values
by Dilek Özkan 18 Aug '22

18 Aug '22

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read that I need to add "--save-posteriors Lesions" to run_samseg to obtain lesion probabilities. 1)In the stats file I can see the value of "Lesions" (0.04) But when I try to see on freeview, it says label=99 (lesion label) has no value. So, I can't see the lesions. 2)There are a few labels related to lesions. For example wm lesions; (498: wmsa, 499: other_wmsa) I have no volume related to these labels neither in my stats file nor on freeview. Should I get only the "Lesions label" for the MS lesion mask? 3)As input, I am using only DIR ımages. I wıill try different thresholds. I have read that by playing mri_binarize and mri_segstats, we can try different thresholds without re-running anything. So, the threshold value required for mri_binarize command refers to the same threshold input in the initial the command of *run_samseg*? Best, Wish

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Re: [Freesurfer] freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz is missing mri_make_bem_surfaces binary
by fsbuild 18 Aug '22

18 Aug '22

External Email - Use Caution Hello John, The mri_make_bem_surfaces command had been put in the attic and removed from all platform builds, but was added back for some OS’s used by a different imaging project back in 2020.  It was not restored for CentOS6 and Ubuntu18 builds.    I don’t think that command  has been updated/supported since ~2001.  We have discontinued CentOS6 builds and I suspect Ubuntu18 will be next since Ubuntu18 LTS (long term stable release) expires in Q1 2023 since both Ubuntu 20 and Ubuntu 22 now have LTS releases. - R. On Aug 17, 2022, at 15:07, Jon Houck <jon.houck(a)gmail.com> wrote:        External Email - Use Caution        Hi,It looks like the ubuntu 18 download for freesurfer 7.3.2 (freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275) doesn't have the binary for mri_make_bem_surfaces.  The file in this version is a bash script that prints the message "error: mri_make_bem_surfaces has been removed from this version of freesurfer. For further information, please post to the help list at  freesurfer(a)nmr.mgh.harvard.edu".. The file isn't listed in 'attic' anymore on github, but for ubuntu 18 seems to be handled as if it was. The tarballs for the other 4 linux distributions are fine and only the ubuntu 18 tarball and .deb have this issue. Is this intentional?  I didn't see anything in the release notes -- apologies if I missed something there.ThanksJon Houck_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FSL course 2022 in Oxford, registration open!
by Rezvan Farahibozorg 18 Aug '22

18 Aug '22

External Email - Use Caution Dear all, We are pleased to announce that registration is open for FSL course 2022 to be held in-person, Sept 19th - 23rd, in Oxford, UK. You can find details and registration info here: https://secure-web.cisco.com/1TQe_KYS57ghqQont7_Je_ygw_ObZFxU1hckwZVjL-w_rG… The course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis. New and existing users of FSL are welcome, as it aims to cover both basic and more advanced topics. The course will include: 1- Lectures: background concepts and practicalities of the analyses; 2- Hands-on practicals: you will learn to carry out analysis on real data. The contents covered are primarily aimed at applications in basic neuroscience and clinical research. Please note that the course will be in-person only, with no remote attendance option. For COVID safety, including masking policy, please refer to the link above. Number of attendees is limited and spots are available on a first-come-first-served basis. Sharing with anyone who might be interested is very welcome! Looking forward to seeing you then, The FSL Course team ------------------------------------------------------------------------- Rezvan Farahibozorg, PhD FMRIB Analysis Group, WIN, NDCN University of Oxford https://secure-web.cisco.com/1pC-HIhu4UpSO09trL3Jx2ZKR6T9E77PamaiEI7XjFmK2h… -------------------------------------------------------------------------

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freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz is missing mri_make_bem_surfaces binary
by Jon Houck 17 Aug '22

17 Aug '22

External Email - Use Caution Hi, It looks like the ubuntu 18 download for freesurfer 7.3.2 (freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275) doesn't have the binary for mri_make_bem_surfaces. The file in this version is a bash script that prints the message "error: mri_make_bem_surfaces has been removed from this version of freesurfer. For further information, please post to the help list at freesurfer(a)nmr.mgh.harvard.edu". The file isn't listed in 'attic' anymore on github, but for ubuntu 18 seems to be handled as if it was. The tarballs for the other 4 linux distributions are fine and only the ubuntu 18 tarball and .deb have this issue. Is this intentional? I didn't see anything in the release notes -- apologies if I missed something there. Thanks Jon Houck

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TRACULA: trac-all -bedp error only with -jobs flag
by Christopher Machle 16 Aug '22

16 Aug '22

External Email - Use Caution Hi Freesurfer team! I am having an issue with the -jobs flag for trac-all -bedp in freesurfer/7.3.0. I ran trac-all -prep with the -jobs flag with no issue, and submitted the commands as jobs on my cluster without error. However, when I try to create the commands for -bedp with the -jobs flag, I get the following error message: ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /projects/dsnlab/shared/tag/nonbids_data/dMRI/tracula/sub-001w01/dmri/nodif_brain_mask.nii.gz pre./projects/dsnlab/shared/tag/TAG_scripts/dMRI/tracula/trac-all_bedp: No such file or directory. The directory in the last line does not exist, so perhaps it's not surprising that I am getting an error with that. However, if I submit the trac-all -bedp command on my cluster directly (without the -jobs flag), it runs without error. I am also able to get the desired output with the -jobs flag for trac-all -path and trac-all -stat (both after running -bedp), so I am not sure what is causing the error using the -jobs flag with trac-all -bedp. Does anyone have any insight as to how I can address this? Ultimately, I'll be running trac-all on a longitudinal data set with many subjects, so I plan to run everything in parallel. I've attached my config file (just one test subject) below. Thanks in advance for the help! Best, Chris

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Password request
by Matiss k 16 Aug '22

16 Aug '22

External Email - Use Caution Hello, I'm looking for the VirtualBox .zip file password. -- Matīss Kore *matiss.kore(a)gmail.com <matiss.kore(a)gmail.com>*

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Two tenure-track positions at the University of Delaware
by Timothy Vickery 16 Aug '22

16 Aug '22

External Email - Use Caution Dear colleagues, The Department of Psychological and Brain Sciences ( https://secure-web.cisco.com/1V_MfdKUpQsoSEbXnYN-yGcswGrjMebYnkelg0ir9iUerM…) in the College of Arts and Sciences at the University of Delaware invites applications for two tenure track Assistant Professor of Psychological and Brain Sciences positions, to begin September 1, 2023. For one position, we seek a scholar with expertise in any specialization of Cognitive Psychology and/or Cognitive Neuroscience. For the second position, we seek a scholar with expertise in computational modeling of cognition and/or computational cognitive neuroscience. Topical areas of specialization within the broad domain of cognition are otherwise open, and we welcome applications from candidates who combine computational approaches with other empirical methodologies (behavioral experiments, psychophysics, neuroimaging, etc.). We especially welcome applicants who conduct research with strong interdisciplinary connections and who can contribute to graduate and undergraduate teaching, advising, and mentoring that support equity and inclusion. This is an outstanding opportunity for a scholar to join and strengthen a thriving, growing community of cognition and neuroscience researchers within the Department of Psychological and Brain Sciences and its research and teaching missions. The Cognitive Area has faculty focusing on spatial representations, vision science and visual cognition, the auditory system, body representations, memory, attention, cognitive control and decision-making. They employ multiple methodologies including neuroimaging at our MRI center, EEG, brain stimulation (TMS), computational modeling, and studies of brain-damaged individuals. Other faculty in Social, Behavioral Neuroscience, and Clinical areas in the Department study closely linked topics such as social cognition, social neuroscience, memory and learning in animal models, and psychological disorders linked to cognition. A strong and growing interdepartmental network of cognitive scientists and neuroscientists is also represented in the Department of Linguistics and Cognitive Science, as well as in departments in the University of Delaware’s Colleges of Health Sciences and Engineering. A new Interdisciplinary Neuroscience Graduate Program provides opportunities to train interdisciplinary scholars and build connections with researchers across departments and colleges. Candidates with strong cross-area and interdisciplinary interests are especially encouraged to apply. 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. Enhanced by state-of-the-art facilities, research is conducted across all seven colleges and numerous interdisciplinary institutes and centers. Relevant staffed facilities on campus include the new 11,600 square foot Center for Biomedical and Brain Imaging (CBBI, http://secure-web.cisco.com/1N4UpvKFpDUlskDL_PbJ2psVoL1m7E5R9Dlr_l5RUGJW-6Q…) housing a 3T Siemens Magnetom Prisma for humans and a 9.4T/20cm Bruker MRI for small animals, an animal housing and research facility attached to the CBBI, a 103,000 square foot Health Sciences Complex, 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 Early Learning Center at UD is a daycare and preschool that supports the academic and research programs of the University as a site for student observation and practicum as well as faculty and graduate student research. The NIH-supported Delaware Center for Neuroscience Research in collaboration with Delaware State University, and the Delaware Health Sciences Alliance (DHSA), a partnership among the University of Delaware, Christiana Care Health System, Nemours/Alfred I. du Pont Hospital for Children, and Thomas Jefferson University, provide infrastructure and opportunity for innovative basic, clinical and translational collaborations. The University of Delaware is located in Newark, Delaware, a charming college town with a busy main street near Wilmington, DE. Newark 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 AND RESPONSIBILITIES: We are seeking two exceptional candidates in cognitive psychology or cognitive neuroscience, one specifically with computational expertise and the other employing any methodological approach. Both candidates should have expertise in one or more topics in cognition. The successful candidate will have a strong history of research and publication of scholarly work and be prepared to teach undergraduate and graduate students. Applicants for this position must have earned a Ph.D. Applicants who are ABD will be considered but must have a granted Ph.D. upon arrival. Responsibilities will include research, teaching and mentorship, and service to the department. PSYCHOLOGICAL AND BRAIN SCIENCES AT UD: The Department of Psychological and Brain Sciences at the University of Delaware ( https://secure-web.cisco.com/1PpFTVridTrcLRQoNQj41f00tcdTgt32i-pDGeMyScvQlX…) is within the College Arts and Sciences. The department is home to roughly 1200 undergraduate majors and 400 minors and offers degrees in both Psychology and Neuroscience. The department is organized around four concentrations of research and graduate training that is highly collaborative and interdisciplinary. Our graduate students and full-time faculty conduct basic and applied research in behavioral neuroscience, clinical science, cognitive psychology and social psychology. We promote the principles of equity and inclusion within our department and beyond through recruitment and retention, graduate training, clinical work, research, service and teaching, as well as through open and productive dialogue. The College of Arts and Sciences at the University of Delaware offers exceptional educational experiences including integrated instruction, research and public engagement. With 24 academic departments and more than 25 centers, programs and institutes, the College serves close to 7,000 undergraduate students and over 1,000 graduate students with CAS majors, but also every single University student through foundational course work. The College’s 600 faculty members emphasize the enduring value of an arts and science education and share a deep commitment to excellence in scholarship and all forms of creative and intellectual expression. The College has departments in the arts, humanities, social sciences and natural sciences, and features outstanding research and teaching facilities. Faculty and staff encourage and support innovative interdisciplinary collaborations and students engage local, national and global audiences through research and creative activity. With annual research expenditures of approximately $38 million and growing, the College currently houses several large, interdisciplinary grants with significant funding from the NIH and NSF. The University of Delaware (http://secure-web.cisco.com/1xtnGU_cxR5bOIA_3R4_HvruiWDN2uXPb-htuSRD5YNlGsr…) is one of the nation’s oldest institutions of higher education, combining tradition and innovation. The university recognizes and values the importance of diversity and inclusion in enriching the experience of its employees and in supporting its academic mission. We are committed to attracting and retaining employees with varying identities and backgrounds, and we strongly encourage applications from educators from under-represented groups. UD provides equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression. TO APPLY: Review of applications will begin on October 1, 2022 and will continue until the position is filled. Applicants should upload a letter of application, curriculum vitae, a research statement, a teaching statement, three representative publications, and contact information for three references at http://secure-web.cisco.com/1bqOo9tvU_psUj61lwtID1LHSsa3r2izdi6lxrLOXq0n7RK… [direct link to application portal: https://secure-web.cisco.com/182WOMsmcGwLCMy84I25CKscscNKG2I0bpwIxfKqrmmZIP…] Please indicate in the cover letter if you believe that you are qualified to be considered for the computationally oriented position (note that this will not exclude you from consideration for the other position). Inquiries, but not application materials, should be emailed to co-Chairs Jared Medina ( jmedina(a)udel.edu) and/or Tim Vickery (tvickery(a)udel.edu) SALARY AND BENEFITS: Compensation packages are highly competitive and commensurate with experience and qualifications. The UD benefits package is one of the best in the nation. EQUAL EMPLOYMENT OPPORTUNITY: The University of Delaware is an Equal Opportunity Employer and encourages applications from members of underrepresented groups. The University's Notice of Non-Discrimination can be found at http://secure-web.cisco.com/1EHVznW1g8ABNs4Ct8AEKh4exxiqS7V3sC7ZcsDXcKlV_rF…

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Large number of false negative MS lesions in SAMSEG
by Cerri, Stefano 16 Aug '22

16 Aug '22

Hi Martin, Can you try to remove the lesion intensity constraint on the T2 data (i.e., by modifying your command with --lesion-mask-pattern 0 1 0) for a couple of cases and let us know if it helps? If not, would you be able to share with us one case where it fails? FYI: you can save a lesion probability map directly by using the flag "--save-posteriors Lesions" so you don't need to try different thresholds. Thanks, Stefano Subject: [Freesurfer] Large number of false negative MS lesions in SAMSEG Date: Sun, 14 Aug 2022 20:54:50 +0200 From: Martin Kavec <martin.kavec(a)gmail.com><mailto:martin.kavec@gmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: Freesurfer mailing list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Hello, I am testing SAMSEG on my group of MS patients. Unfortunately, even when dropping threshold to 0.005 I have large number of false negative lesions left behind by SAMSEG (80% in about 75 cases I tried), which are clearly visible lesions. I ran/checked registration between inputs, which is typically very good to excellent. Images are all 3D acquisitions , mprage, flair, and t2 with ~1 mm3 isotropic voxel. Here is the command, which I ran: run_samseg --input mprage_reg.nii.gz flair.nii.gz t2_reg.nii.gz --pallidum-separate --lesion --lesion-mask-pattern 0 1 1 --threshold 0.005 --output samseg_threshold_0.005 and example of the lesion in occipital white matter in sagittal and axial orientations. [image.png] [image.png] I would very much appreciate any leads as to how to improve the segmentation. Thanks, Martin

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Freesurfer August 2022