Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

misalignment after converting to gifti
by Jiaen Liu 31 Jul '24

31 Jul '24

External Email - Use Caution I converted surface data in the cortex to surf.gii and loaded the data in connectom workbench. But the cortical curvature aligned well with the T1 image in Freesurfer doesn't align well in the workbench. I used mris_convert for the conversion. I'm wondering if I missed certain parameter Below the left is the workbench display and right is in Freesurfer. Thanks! [cid:image001.png@01DAE359.488E22C0] Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://labs.utsouthwestern.edu/liu-jiaen-lab> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Question: Recon-all Using T1/T2 Mutual Information
by Edwards, Vincent 31 Jul '24

31 Jul '24

External Email - Use Caution Hello Freesurfer team! We are editing brain scans using T1/T2 mutual information to improve the original image. Are the recon-all flags the same with as they would be when editing using only the T1 images (i.e., recon-all -cp, -pial, -wm), or are there additional flags are needed after editing? Thank you, Vincent Edwards

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Data Analyst Position at University of Miami Miller School of Medicine
by Otero Ospina, Andrea 30 Jul '24

30 Jul '24

External Email - Use Caution Hi I hope this mail finds you well. Could you please post a job announcement to your mailing list? I'm already inscribed in your mailing list. Best regards Data Analyst Position at University of Miami Miller School of Medicine The Gabbay Laboratory, located within the Department of Psychiatry & Behavioral Sciences at the University of Miami Miller School of Medicine, is seeking well-qualified applicants for the role of data analyst. This position will focus on processing human neuroimaging datasets, including anatomical and functional magnetic resonance imaging (MRI), MR spectroscopy, and related biological measures. Candidates should hold an MS or equivalent degree in the fields of computer science, neuroscience, psychology, radiology, engineering, biostatistics, or a related field. Candidates with a BS-level degree and significant prior experience in a similar role will also be considered on a case-by-case basis. Proficiency with one or more major programming languages used in bioscience (i.e. MATLAB, Python, R) as well as Unix/Linux environments is expected. Familiarity with neuroimaging software (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench) and with scientific/cluster computing is preferred. The primary responsibility for this role will be to analyze neuroimaging data from multiple ongoing and recently concluded research projects; additional tasks will entail assisting with MRI data collection and manuscript drafting. The data analyst position will be supervised by Vilma Gabbay, MD and Benjamin Ely, PhD. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in high-risk populations (e.g. adolescents, people living with HIV, cannabis users) using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding for active and exploratory studies. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners with cutting-edge accelerated and multi-echo fMRI sequences; high-performance scientific computing clusters; and an extensive library of analytic and statistical software. The PIs are fully committed to fostering a productive mentorship environment, with opportunities for career advancement including manuscript coauthorship, conference attendance, and training in grant writing. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. University of Miami is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard rates posted by University of Miami. Andrea Otero, M.D. Clinical Research Coordinator Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu<mailto:njh115@med.miami.edu> Phone: 305-243-7086 [cid:17329a4c-56a0-4992-a963-79be54c54353] [cid:47ee1259-91e2-4e19-b42d-696df19c9a75]<https://outlook.office.com/bookwithme/user/0e91508c58304aa8bcb3ea3526547a26…> Book time to meet with me<https://outlook.office.com/bookwithme/user/0e91508c58304aa8bcb3ea3526547a26…>

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FreeSurfer Question
by Selena Gangaram 29 Jul '24

29 Jul '24

External Email - Use Caution Hi, I hope you are doing well, I subscribed to your mailing list to ask my question! I was wondering if you knew the reason as to why my extraction code in FreeSurfer listed regions such as "Whole_hippocampal_body" amongst other brain regions twice in my stats files. In my excel stats files I have two Whole_hippocampal_body and I wasn't sure what the two different values meant. Please help! Thank you!!! Best, Selena

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Inquiry About Calculation of Integrated Rectified Gaussian Curvature in mris_anatomical_stats
by littlepotato 29 Jul '24

29 Jul '24

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am currently using FreeSurfer's mris_anatomical_stats tool for my research, and I have encountered a question regarding the calculation of the Integrated Rectified Gaussian Curvature value reported in the .stats files, such as lh.aparc.stats. Specifically, I would like to understand the detailed methodology used to compute the Integrated Rectified Gaussian (Mean) Curvature. My current understanding is that this value might be derived from the mean of the absolute values of the Gaussian curvature multiplied by the vertex areas, similar to the following calculation: mean(abs(lh.smoothwm.K.crv)×lh.area)\text{mean}(\text{abs}( \text{lh.smoothwm.K.crv} ) \times \text{lh.area}) Could you please confirm if this is correct? If not, I would appreciate it if you could provide a detailed explanation of the exact steps and calculations involved in deriving this metric. Thank you very much for your time and assistance. I look forward to your response. Best regards, Amber Lin Researcher Tianjin Medical University lly_scu(a)163.com

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ssistance needed: Aligning existing FreeSurfer segmentation with new T1 image
by Owusu-Ansah, Maame 25 Jul '24

25 Jul '24

External Email - Use Caution Dear FreeSurfer team, I'm working on a project where I need to align an existing FreeSurfer segmentation (from an older T1 image) with a the same T1 image of the same subject, but it is debiased and in a different atlas space. The goal is to leverage the manual edits and refinements made in the original FreeSurfer output while utilizing the improved image quality of the new T1 scan. Current approach: 1. Using mri_robust_register to align the old FreeSurfer T1 to the new T1 image 2. Applying the resulting transformation to all FreeSurfer volumes (mri/*.mgz files) 3. Transforming the surface files using mri_surf2surf 4. Running recon-all -autorecon2-cp -autorecon3 on the transformed data Main Issue: After applying our current approach, we've noticed that while the volume files (mri/.mgz) seem to align well with the new T1 image, the surface files (surf/.pial, surf/*.white, etc.) are not aligning properly. This misalignment is causing discrepancies in our cortical measurements and affecting downstream analyses. Questions: 1. Is our approach appropriate for maintaining the quality of the original segmentation while adapting to the new T1 image? 2. Why might the surface files be misaligned when the volume files seem to align correctly? 3. Are there alternative methods or additional steps we should consider to ensure proper alignment of both volume and surface files? 4. How can we ensure that manually edited regions in the original segmentation are preserved, especially for surface-based edits? 5. Are there specific quality control steps you'd recommend for verifying both volume and surface alignment? Any guidance, alternative approaches, or explanations you could provide would be greatly appreciated. Thanks, Maame ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Assistance needed: Aligning existing FreeSurfer segmentation with new T1 image
by Owusu-Ansah, Maame 25 Jul '24

25 Jul '24

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Issues for longitudinal pipeline-based process
by Yoonho Hwang 24 Jul '24

24 Jul '24

External Email - Use Caution Dear FreeSurfer developers, Hi, Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-up (scanner 1), 2nd follow-up (scanner 2)]. I applied the longitudinal pipeline of FreeSurfer to the data as follows: 1. Cross-sectional process for each time point 2. Create template (recon-all -base long_base -tp long_tp1 -tp long_tp2 -tp long_tp3 -all -parallel -openmp 4) 3. Longitudinal process In process 2, I encountered the following warning, but completed the entire process without errors. ******************************************************************************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ******************************************************************************* There are resolutions of our data for each time point: - Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180) - 1st follow-up (scanner1, 512 x 512 x 180) - 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Can I ignore the warning? Or is there anything I need to fix before doing process 3 (longitudinal process)? Also, could you please give me any suggestions on longitudinal analyses? Thank you very much Sincerely, Yoonho

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Scalp mask
by Francesco Lomi 22 Jul '24

22 Jul '24

External Email - Use Caution Hi everybody, Do you know how to create a scalp mask file with freesurfer? Thank you in advance Francesco

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Negative voxel ranges
by ERNEST KISSI 22 Jul '24

22 Jul '24

External Email - Use Caution Dear fresurfer team, Please I want to extract the intensity of a voxel 48, -56, -34. But my voxel ranges of my image does not include negative values. Is there a way to make the ranges cover these values. Thanks 👍.

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