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[WARNING: ATTACHMENT UNSCANNED]Help: Using a Different Atlas for Anatomical ROI Analysis
by Flanagan, Shawn D 28 Nov '21

28 Nov '21

External Email - Use Caution Hello, I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to "run recon-all on the AAL anatomical T1w volume template". At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines? In summary, I am wondering if you can "walk me through" the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time. Best, Shawn --- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center 3860 South Water Street Pittsburgh, PA 15203 sdf29(a)pitt.edu<mailto:sdf29@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1xPYTwm1twYgyoLhqQPj3hQ3mM2mqTCUs_emm18SlHI78wP…>

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SynthSeg
by AJ 28 Nov '21

28 Nov '21

External Email - Use Caution Hi Thank you for your help. I ran SynthSeg successfully. How do you derive sbTIV value ? Could one use sbTIV from SAMSEG? Many thanks AJ

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Freeview.app crashing
by ChristianBauer 26 Nov '21

26 Nov '21

External Email - Use Caution Dear Freesurfer experts, I am having issues with opening Freeview. I am currently using Freesurfer v.7.2.0 and I had no problems setting up Freeusurfer and Freeview on my Desktop computer. However, I have had issues with Freeview crashing on my Mac laptop every now and then and now I cannot open Freeview at all The error message I am getting is a s follows /Applications/freesurfer/7.2.0/bin/freeview: line 2: 3185 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ I have tried downloading and reinstalling Freesurfer several times as well as trying the stand-alone version. I have also changed the license file as was previously suggested by one of your team. Any advice would be greatly appreciated. Thanks in advance, Christian

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Converting .trk files in mini space to nifti using dorm_trk2trk
by Schaechter, Judith D. 23 Nov '21

23 Nov '21

Hi, I'd like to convert *trk files that are in mni space to nifti files using dmri_trk2trk. The *trk files are here: /autofs/vast/freesurfer/centos7_x86_64/7.2.0-beta/trctrain/hcp/mni Attempts so far (that have failed) are: dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_template_identity.mat with MGH35_HCP_FA_template_identity.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MGH35_HCP_FA_template.nii.gz -omat MGH35_HCP_FA_template_identity.mat dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat with MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MNI152_T1_2mm_brain.nii.gz -omat MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat Thanks in advance for your help! Judith ******************************************************* Judith D. Schaechter, Ph.D., M.S.P.T. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital, Harvard Medical School 13th Street, Building 149, Room 2301 Charlestown, MA 02129 Office 617-726-5622 | Cell 781-752-6247 | Fax 617-726-7422 Email jschaechter(a)mgh.harvard.edu

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Freeview grey matter, white matter and Tracula outputs
by Zeng, Qi 23 Nov '21

23 Nov '21

External Email - Use Caution Hi, If I want to freeview fully segmented grey matter, white matter, and Tracula outputs, are the following commands correct to the request? # to visualize the segmented cortical outputs freeview -v mri/aparc+aseg.mgz Question: why is one hemisphere brighter than the other? How can I adjust so that they are equally bright? # to visualize the segmented subcortical outputs freeview -v mri/aseg.mgz Question: why is only one hemisphere showing and how to add the other one? $ to visualize AD. RD, FA and color-coded each freeview -v dmri/dtifit_FA.nii Question: I cannot find the nifti outputs of AD and RD (however, the stats generated). where can I find it? Is there an example of how to color-code them for freeview? Thank you! Best, Jackie

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[WARNING: ATTACHMENT UNSCANNED]Using a Different Atlas for Anatomical ROI Analysis
by Flanagan, Shawn D 23 Nov '21

23 Nov '21

External Email - Use Caution Hello, I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines? In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time. Best, Shawn --- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center 3860 South Water Street Pittsburgh, PA 15203 sdf29(a)pitt.edu<mailto:sdf29@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1w-f2b1Sv8FoWJqjWBtRI_gzdJ3kwmFPg5ehq75ANa6Is4a…>

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Pipeline errors - matlab
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 22 Nov '21

22 Nov '21

External Email - Use Caution Hello Freesurfer experts! Hope that you are all well. I am having errors when running hippocampal subfields and thalamic subfields. When in the error log for the hippocampal pipeline, this is part of the error that I got: *MATLAB is exiting because of fatal error* */Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 7498 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args* *Darwin CCAPSY-0GYM0XV 20.6.0 Darwin Kernel Version 20.6.0: Mon Aug 30 06:12:21 PDT 2021; root:xnu-7195.141.6~3/RELEASE_X86_64 x86_64* *T1 hippocampal subfields exited with ERRORS at Fri Nov 12 14:26:43 EST 2021* Please let me know if additional info is needed. Thank you so much, Alex

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Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School
by Margiotta, Kathryn Nicole 22 Nov '21

22 Nov '21

[cid:ffcafe71-529c-423a-8564-7c00e4b3ff4d] Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School Postdoctoral positions are available under the mentorship of Dr. Matthew D. Sacchet within the Meditation Research Group of the Center for Depression, Anxiety, and Stress Research at McLean Hospital/Harvard Medical School. These positions are fully supported by NIH and Foundation funds. The Meditation Research Group (Directed by Dr. Sacchet; https://meditation.mclean.harvard.edu/) advances the science of meditation in both clinical and non-clinical contexts and the neuroscience of depression. The Group’s studies span and integrate affective and cognitive neuroscience, clinical psychology and psychiatry, computer science and related computational disciplines, contemplative and religious studies, neuro- and micro-phenomenology, human neuroimaging, and psychoneuroimmunology including epigenetics and stress physiology. The Center for Depression, Anxiety and Stress Research (CDASR; Directed by Dr. Diego A. Pizzagalli; http://cdasr.mclean.harvard.edu<http://cdasr.mclean.harvard.edu/>) is a vibrant research center with over 40 scientists/staff/students that embraces a multi-disciplinary approach to improve our understanding of the psychological, environmental, and neurobiological factors associated with depression, anxiety, and related disorders across the lifespan. Successful candidates will be expected to lead and collaborate on projects that advance one or both of the neuroscience of depression and/or the neuroscience of meditation. The candidate will have access to extensive existing and newly acquired data across these two domains. Opportunities will be available to pursue independent research and interdisciplinary collaborations across Harvard Medical School and beyond. Depending on research focus, candidates will have access to research-dedicated human MRI scanners (3T, 4T, and 7T) as well as two high-density EEG systems. Qualifications: A strong background in functional MRI analysis is required. Expertise in clinical neuroscience or contemplative neuroscience is desired though not required. Additional experience with a second imaging modality (notably EEG) and in computational approaches (e.g., computational modeling, machine learning) will also be considered. To apply, send a CV, a cover letter describing research interests, as well as names and email addresses of three references to Matthew D. Sacchet (msacchet(a)mclean.harvard.edu<mailto:msacchet@mclean.harvard.edu>). Review of applications will begin immediately (expected start date: early 2022, although other timeframes may be possible). About McLean Hospital and Harvard Medical School Since 1811, McLean Hospital has been a world leader in scientific investigations and treatments of mental illnesses as well as in training generations of scientists and clinicians. McLean Hospital is the flagship psychiatric affiliate and teaching hospital of Harvard Medical School. McLean Hospital maintains the largest program of research in neuroscience and psychiatry of any private psychiatric hospital in the United States. McLean Hospital has been ranked as America’s best freestanding psychiatric hospital for 18 consecutive years by U.S. News and World Report. U.S. News and World Report has consistently ranked Harvard Medical School as the best Research Medical School with the best Psychiatry Program. McLean Hospital is in Belmont, Massachusetts, approximately 5 miles from Boston. McLean Hospital is located in Belmont, Massachusetts, approximately 5 miles from Boston. McLean Hospital, which is an affiliate of Harvard Medical School, is an Equal Opportunity Employer. As an equal opportunity employer, McLean seeks qualified candidates for all posted employment opportunities without regard to race, color, age, religion, gender, national origin, disability or veteran status. McLean particularly welcomes applications from minorities, women, and persons with disabilities.

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PhD Position Available @ University of Delaware: Movement Disorders/Parkinson's Disease Research
by Roxana Burciu 22 Nov '21

22 Nov '21

External Email - Use Caution The Motor Neuroscience and Neuroimaging Laboratory in the Department of Kinesiology and Applied Physiology at the University of Delaware ( https://secure-web.cisco.com/1FGUBbOfcKBczlqb5RsAtMzP59F-DjBkVa-NfDgzN_TBY1…) led by Dr. Roxana Burciu, is seeking motivated and enthusiastic students interested in pursuing a PhD in Neuroscience starting in Fall 2022. The lab aims to improve our understanding of human neural control of movement and leverage this information to improve motor function, mobility and the quality of life of individuals with movement disorders such as Parkinson’s disease. Students will work in an innovative research program that combines advanced functional and structural brain MRI techniques (task-based and resting state fMRI, arterial spin labelling, diffusion MRI, SWI), behavioral protocols and genetics to understand how the brain and behavior change in people with Parkinson’s disease and those at risk of developing the disease. The lab has access to UD’s Center for Biomedical and Brain Imaging which houses a 3T Siemens Magnetom Prisma whole-body MRI scanner and a 9.4 Bruker Biospec 94/20, designed for pre-clinical MR imaging and MRI research. The lab is also integrated with several other research laboratories studying the neural control of movement in healthy and Parkinson’s disease, which provides a rich scientific and collaborative community. PhD positions are funded through a combination of teaching and research assistantships. Requirements: - Have a background in neuroscience, biomedical engineering, kinesiology, psychology, or biomedical sciences. - Previous MRI experience is desirable. Have some experience with signal processing, bash, MATLAB or similar programming languages. - Be team-minded, flexible with the required tact and sensitivity for working with patients with neurological disorders. Potential applicants should contact Dr. Roxana Burciu at rgburciu(a)udel.edu with a brief email expressing their research interests, and a current CV. -- *Roxana G. Burciu, Ph.D. | **Assistant Professor* Department of Kinesiology and Applied Physiology, University of Delaware 347 STAR Tower, 100 Discovery Blvd., Newark DE, 19713 E: rgburciu(a)udel.edu | T: (302)-831-3066 | F: (302)-831-8813 Motor Neuroscience and Neuroimaging Lab: https://secure-web.cisco.com/1FGUBbOfcKBczlqb5RsAtMzP59F-DjBkVa-NfDgzN_TBY1… <https://secure-web.cisco.com/1w_QDOJZ2yFKkxLhwU9QrysW0rqX5hzSItrB2IEzWHNvfa…>

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Postdoctoral position in Developmental/Affective/Clinical Neuroscience
by Jeffrey Spielberg 22 Nov '21

22 Nov '21

External Email - Use Caution Dr. Jeffrey Spielberg is accepting applications for a *Postdoctoral Researcher position* in the *Connectomics of Anxiety and Depression* Lab at the University of Delaware. The researcher will contribute to an ongoing NIMH-funded R01 grant examining longitudinal change in brain networks that contribute to anxiety development during early adolescence, with a focus on pubertal hormones. The ideal candidate will have a strong background in programming and MRI analysis, along with an interest in adolescent development, emotion/motivation, and/or anxiety, although all applications are encouraged. Clinical training or experience with network analysis methods are not required, but would be considered an asset. Applications from any area of Psychology/Neuroscience are encouraged, although previous experience with human MRI is necessary. The primary duties of the postdoctoral researcher will be to analyze MRI data and write manuscripts for publication. In addition, the researcher will have the opportunity to learn and apply cutting-edge network-analysis methods (e.g., graph theory) to understand the network basis for anxiety. The position would last for a two-year period with potential for renewal. If you are interested in being considered for the position, please send a current CV, a brief statement of interest that outlines your qualifications for the position, reprints of selected papers, and the names of three professional references to Dr. Jeffrey Spielberg at jmsp(a)udel.edu. For more information on the lab’s work, see http://secure-web.cisco.com/10kRxO4QDT9UHmYJygXW-LnOe5rPLvNlHrCty61ZS9vJPOg… *QUALIFICATIONS:* - Ph.D. in psychology, neuroscience, or related disciplines - Experience processing and analyzing structural, functional, and/or diffusion MRI data - Proficiency in programming (e.g., MATLAB, python) - Previous human MRI publications - Interest in adolescent development, emotion/motivation, and/or anxiety - Clinical training (e.g., SCID/KSADS administration) and/or experience with network analysis (e.g., graph theory) are not required, but would be considered an asset -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078 Email: jmsp(a)udel.edu Website: http://secure-web.cisco.com/12t4roXdLMzWMowFXG4PN_M7hKCruxhrARdichNITr9XaE3…

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