Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
by Nikita Nogovitsyn 12 Jun '18

12 Jun '18

External Email - Use Caution HI I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere. Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv Thanks Nikita

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Poor anterior temporal lobe surfaces
by Meaghan Perdue 12 Jun '18

12 Jun '18

External Email - Use Caution Hello Freesurfer experts, I tried to send this out last week, but I'm not sure whether it made it to the list. I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Difference between Freesurfer and Voxel Based Morphometry
by Miguel Ángel Rivas Fernández 12 Jun '18

12 Jun '18

External Email - Use Caution Hi Freesurfer developers, I´m starting in structural MRI analysis with Freesurfer and i would like to know what is the main difference between freesurfer and the voxel based morphometry approach. It is more appropiate to use a method for some specific analysis? Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández*

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ExploreDTI Workshop in September 2018
by Szabolcs David 11 Jun '18

11 Jun '18

External Email - Use Caution ExploreDTI Workshop - A course on processing, analyzing, and visualizing diffusion MRI data When: 10-12 September, 2018 Where: Utrecht, Netherlands Details: http://www.exploredti.com/workshop See you soon in the early Dutch autumn ;) Best, Szabolcs

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Offset in surface rendering
by Laura Jeyaseelan 11 Jun '18

11 Jun '18

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to convert a 3D label mask (saved as a .nii.gz image) into a surface rendering (saved as .surf.gii). *import nipype.interfaces.freesurfer as fs* *mc = fs.MRIMarchingCubes()* *mc.inputs.in_file = './lung.nii.gz'* *mc.inputs.label_value = 1* *mc.inputs.out_file = 'fs_lung.surf.gii'* *mc.run() * The code above does not throw any errors, but there appears to be an offset when viewing the surface reconstruction using the Papaya viewer on the browser. If I try creating the surface using Papaya's companion software Mango there is no offset seen. Does anyone have any ideas to trouble-shoot this issue? I've attached screenshots to show the difference: FreeSurfer generated .surf.gii file viewed on Papaya: Mango generated .surf.gii file viewed on Papaya: Thanks, Laura

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Posting to FreeSurfer Support List
by Laura Jeyaseelan 11 Jun '18

11 Jun '18

External Email - Use Caution Hello, I'd like to be able to post to the FreeSurfer support list using laura(a)voxelcloud.io. Thanks, Laura

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Using mri_convert with different scan lengths
by Lori Sanfratello 11 Jun '18

11 Jun '18

External Email - Use Caution Hello, I would like to use mri_convert to reslice my images. However, I have scans of different duration and it seems that when I do the following: mri_convert fileA.nii fileA_resliced.nii -rl fileB.nii it not only changes the spatial dimensions but also the time dimension. Is there a way to retain the original timing? Many thanks, Lori -- Dr. L. Sanfratello, PhD Assistant Professor of Trans. Neuroscience The Mind Research Network, 1101 Yale Blvd NE Albuquerque, NM 87106 505 272-5557

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FreeSurfer Longitudinal analysis
by Глеб Макшаков 11 Jun '18

11 Jun '18

External Email - Use Caution Dear all, I’ve just started using FreeSurfer and I need your advice. I have two series of images made 1 year apart from each other. Is it correct to use a Longitudinal Stream to process those images instead of simple cross-sectional counting and then estimating the difference in volumes between them? Regards, Gleb Makshakov MD, neurologist City Clinical Hospital 31 City Center of Multiple Sclerosis and AID Neurology Department of FSBEI HE I.P.Pavlov SPbSMU MOH Russia gleb.makshakov(a)gmail.com +79213912101

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Full-Time Research Assistant Position in Clinical Neuroscience at Ohio State University
by Herring, Elizabeth J. 11 Jun '18

11 Jun '18

External Email - Use Caution Posted on behalf of Dr. Ruchika Prakash: Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University The Clinical Neuroscience Lab, in the Psychology Department, within the College of Arts and Sciences, seeks a Research Assistant 1-Social to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash. The Research Assistant 1 assists in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitates recruitment efforts between the laboratory and community partners for human subject payments; conducts neuropsychological assessment sessions with clinical populations; assists with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB; supervises undergraduate research assistants. Position available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com/postings/86981 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html 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.

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Analyzing slice data with freesurfer?
by John Absher 11 Jun '18

11 Jun '18

External Email - Use Caution We are attempting to analyze archival MRI data obtained during routine clinical care. Unfortunately, the standard clinical MR sequences do not include 3D volumes. Will the freesurfer algorithm work on slice data so that each slice could be marked with the pial and white matter boundaries? Then, the next question is how to apply seg and parc templates to analyze correctly defined subcortical structures, and cortical regions? Has anyone tried to do this type of archival data analysis? Unfortunately, our standard sequences do not include 3D volumes, so to do the retrospective work we'll need a workaround. Thank you. John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Freesurfer June 2018