Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

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by macara.p＠libero.it 06 Mar '17

06 Mar '17

96 Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} Open position: PhD in “multimodal imaging to understand vulnerability for developing schizophrenia” Developmental Imaging and Psychopathology laboratory Campus Biotech Starting date: to be defined Working environment: In the context of a longitudinal study started 15 years ago, we perform a multidisciplinary evaluation of patients with the 22q11.2 deletion syndrome, a neurogenetic condition that confers a high-risk of developing schizophrenia. Our protocol includes acquisitions of structural, functional and diffusion images and their analysis with gold-standard neuroimaging tools. By investigating morphological and connectivity alterations associated to the microdeletion and to the onset of psychotic symptoms, we aim at identifying potential biomarkers for the development of schizophrenia. Tasks of the PhD student: - To work in collaboration with clinical and engineering departments for the development and application of new methodologies; - To analyze complex multimodal and longitudinal fMRI data; - To participate to MRI data acquisition; - Manuscripts redaction. Methods employed in the lab: Cortical morphometry (thickness, gyrification), voxel-based DTI, tractography, resting-state fMRI, graph theory, pattern recognition, multivariate pattern analysis (MVPA). Toolboxes employed in the lab: Matlab, SPM, FSL, FreeSurfer, connectomemapper. Academic requirements: We are looking for young, nearly graduated students with a master degree in medicine, psychology, biology, sciences, neurosciences or equivalent title. Expertise in brain imaging and/or programming is not mandatory but highly preferred. Contact: The candidature (motivation letter, CV, copy of the diploma and graduations, eventually letter of recommendation) has to be sent preferentially by email to the following addresses: Maria Carmela PADULA (maria.padula(a)unige.ch) Maude SCHNEIDER (maude.schneider(a)unige.ch) Campus Biotech Chemin des Mines 9 1202 Genève 022/379.12.28

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mri_vol2surf error in FS6
by Fred Lado 05 Mar '17

05 Mar '17

Dear FreeSurfer Experts, I just installed FS6 and encountered the following error, which I can replicate by just entering “mri_vol2surf” on the command line: /Users/fred 3> mri_vol2surf dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I am running Mac OS X El Capital 10.11.6, after searching the archives I also tried turning off SIP, which did not help. Any other advice? Thanks, Fred Fred Lado, MD PhD Director, Epilepsy - Central and Eastern Regions Northwell Health 917-608-1881 (mobile) 516-325-7000 (practice) 516-325-7001 (fax) flado(a)northwell.edu Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately.

2 1

VISUALIZATION OF INTER-SUBJECT REGISTRATION
by Marco Martinolli 05 Mar '17

05 Mar '17

Dear Freesurfer users, I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc).What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know. By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool! Cheers,Marco

2 3

panning Freeview on MacBook Pro
by me＠marychin.org 04 Mar '17

04 Mar '17

Hi, How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook Pro (Early 2011). On https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsag… it reads: You can pan across the data, which is especially useful when zoomed in. To do so while in Navigate mode navigate.gif , Voxel Edit mode voxel_edit.gif , or Recon Edit mode recon_edit.gif click and hold the scroll button on the mouse while moving the image. Alternatively, you can use the arrow keys on the keyboard. When using the arrow keys, know that when you scroll up, down, right or left, the actual label moves around, not the screen. I have tried the touchpad, with and without cmd, alt, fn, shift, ctrl... Also tried the arrow keys. Thanks, mary

3 4

ACPC alignment before or after running on Freesurfer?
by Lee Subin Kristine 03 Mar '17

03 Mar '17

Dear Freesurfer team, This may sound like a bit of a small question, but I could not find any exact answer elsewhere. Does the exact orientation of the input image have much effect on the accuracy of the segmentation in Freesurfer? It seems that some people apply ACPC alignment to the output of Freesurfer, so I am confused as to which order would be optimal. Thank you in advance, Kristine

3 2

Reslice image
by John Anderson 03 Mar '17

03 Mar '17

Dear experts: I have nifti file with 96 slices. I want to re-slice it to form nifti file with 200 slice. Are there any tools in Freesurfer that can help to achieve this? Many thanks for any suggestion John

1 0

Hippocampal overestimation 5.3 vs 6.0
by Dawn C. Matthews 03 Mar '17

03 Mar '17

Eugenio and Freesurfer team, Many thanks for responding to these questions. My question relates to hippocampal volume overestimation. I believe that a European team recently evaluated the performance of hippocampus segmentation using different automated segmentation methods including Freesurfer on more than 400 scans from several previous studies, and found that Freesurfer and FSL-FIRST may include tissue that is not part of the hippocampus. Liedlgruger et al, “Variability Issues in Automated Hippocampal Segmentation”, 2017, also reported that Freesurfer overestimated volumes vs. other methods tested. I wondered if version 6.0 addresses the overestimation issue? It appeared that the FS 6.0 release web page figure (which showed the hippocampal portion of an MRI at left, the 5.3 subfield segmentation in the middle, and the 6.0 subfield segmentation at right) showed that a portion of gray tissue superior to hippocampus was included in the 5.3 segmentation but not in the 6.0 version – was that an example of 5.3 overinclusion, addressed in 6.0? Thank you again for your help and for the team’s continued advances. Dawn

2 1

Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)
by randrews＠admdx.com 03 Mar '17

03 Mar '17

1 0

LGI: "Error using freesurfer_read_surf (line 90) could not open surface file lh.pial."
by Louise Baruël Johansen 03 Mar '17

03 Mar '17

Hi FreeSurfer developers, I’m trying to compute the gyrification index using the command: recon-all -s subject1 -localGI But I get the following error message when trying different subjects and with different versions of matlab: (the left hemisphere - not the right - invokes the error) —— FREESURFER_READ_SURF [v 1.2 ] Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); ERROR: find_corresponding_center_FSformat did not complete successfully! Linux big22 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ---- I can’t find a solution to this error on the mailing list… FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thanks, Louise

1 0

to evaluate volume and thickness of the amygdala using asegstats2table
by Gwang-Won Kim 02 Mar '17

02 Mar '17

2 1

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