Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Re-running recon-all in V6 {Disarmed}
by Kevin Aquino 30 Dec '16

30 Dec '16

Hi all, When V6 is released I'd want to re-run all my (10) subjects through recon-all again (they were processed with v6 alpha). I'd like to keep all my wm edits, mask and control points, is it as easy as just running recon-all on the same folder again? They are 0.7mm so I'd like to keep all the corrections. Cheers! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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under estimation of white matter and pial surface
by miracle ozzoude 29 Dec '16

29 Dec '16

Hello Freesurfer, I was wondering if anyone knows how to correct an underestimation of white matter and pial surface outputs from freesurfer. I attached an image showing the error. Thanks. Best, Paul

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Fwd: localGI bug
by David Groppe 28 Dec '16

28 Dec '16

Dear FreeSurfer Developers, I think there is a bug in FreeSurfer's MATLAB code that is used to compute the local gyrification index. Specifically, when I run this command: *recon-all -s PT001 -localGI* I get the following error: *face 115000 / 118360mesh_outer = vertices: [59182x3 double] faces: [118360x3 double] facesOfVertex: [59182x1 struct]preparing pial mesh structure ......searching for mesh edges...done (171.44 sec).... creating path file for vertex 1 / 59182area file for outer ROIs saved at 1In an assignment A(:) = B, the number of elements in A and B must be the same.Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);* *>> ERROR: make_roi_paths did not complete successfully!* I ran the command in debugging mode and *x* and *yi *are both empty variables. I am using a freshly installed version of the Lion OS X 10.7 (64b Intel) version of FreeSurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg; freesurfer-Darwin-lion-stable-pub-v5.3.0) and am running on OS 10.11.6 using MATLAB version R2015b (8.6.0.267246). The recon-all.log is attached. Let me know if there is any further information I can provide and thanks for producing such a fantastic piece of freeware. -David Groppe

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recon-all Line search failed
by Ladan Shahshahani 28 Dec '16

28 Dec '16

Dear experts, I tried running recon-all for a subject and it exited with the following error: LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and my operating system is 14.04.1-Ubuntu. attached is the recon-all.log. Best, Ladan

2 1

postdoc in computational neuroimaging (method development)
by Martin Reuter 28 Dec '16

28 Dec '16

Hi all, I wish everyone a successful new year 2017! Please pass along this job offer for a postdoc position in my group in Bonn, Germany, to anyone interested and feel free to contact me with any questions. Thanks, Martin Reuter The German Center for Neurodegenerative Diseases (DZNE) in Bonn, Germany is looking for a Postdoc (f/m) in Computational Neuroimaging – Code 1427/2016/12 to join the research group of Prof. Martin Reuter. Research projects will focus on developing image analysis, geometry processing and machine learning methods for the automatic analysis of multi-modal human MRI data, primarily with the aim to extract imaging biomarkers that can be leveraged to both understand or diagnose neurodegenerative disease and to provide a rational framework for targeting and monitoring therapy. Prof. Martin Reuter, has recently joined the DZNE and simultaneously holds a faculty position at the Martinos Center, MGH, Harvard Medical School, Boston, USA with an affiliation at the Massachusetts Institute of Technology CSAIL. He is the principal developer of the longitudinal processing framework of the software package FreeSurfer, providing a suite of tools for the automated analysis of brain MRI data to a world-wide user base. He and his team have, furthermore, introduced novel approaches for neuroanatomical shape analysis and computer-aided diagnosis and prognosis of neurodegenerative disease. Your profile: We seek a postdoctoral candidate with a Ph.D. in computer science, engineering or mathematics with interest in image and geometry processing and with solid programming skills in C/C++, Python, Matlab, R, shell scripting, GPU (parallelization). The ideal candidate would have knowledge in computational neuroimaging or biomedical engineering and considerable expertise in methodological development of quantitative MRI analysis, e.g. registration, segmentation, Bayesian modeling. Experience with big data analysis, cloud computing and machine learning is an asset. Knowledge of state-of-the-art data analyses techniques and neuroimaging software, including FreeSurfer, ANTS, FSL is also appreciated. Highly motivated individuals with a record of productive research are encouraged to apply. The working language is English. We offer: Integration into the computational imaging environment at DZNE and interdisciplinary interactions with other institutes in Bonn and abroad (e.g. Harvard Medical School). Recently opened DZNE Research Facilities at Bonn Venusberg, hosting a state of the art neuroimaging center with 7T and 3T MRI scanners, as well as computational infrastructure supported by experienced IT specialists and physicists. A rich set of high-quality MR data and applied research questions through collaboration with the Rhineland Study, a prospective deeply phenotyped longitudinal cohort study with up to 30.000 participants. A strong mentoring program for career development is provided. An international environment characterized by a strong focus on science and research. Bonn, located at the Rhine river in proximity to the Cologne metropolitan area, has a very high quality of life, with an international student, research and business community. The position is initially available for 2 years. Employment, payment and social benefits are determined by the Public Sector Collective Agreement (Tarifvertrag für den öffentlichen Dienst – TVöD Bund). The DZNE is an equal opportunity employer and especially welcomes and encourages disabled individuals to apply. You will obtain special skills and knowledge for your scientific qualification during your activities at DZNE. Interested candidates should send their full application documents in a single PDF with subject CODE 1427/2016/12 via email to application(at)dzne.de . Please include a CV, contact information of two referees, a brief statement describing your personal qualifications and future research interests (up to 1 page), and a list of publications highlighting up to three most important ones. Informal enquiries may be directed to Martin Reuter (martin.reuter(at)dzne.de <>). Information about previous activities of the group can be found at http://reuter.mit.edu <http://reuter.mit.edu/> Applications are due January 25 2017

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Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream
by Tamara Tavares 28 Dec '16

28 Dec '16

Thank you for your reply Dr. Reuter. I have about 3 scans in which the acquisition parameters are slightly different between time 1 and time 2 which probably contributes to these differences. Do you recommend that I do not use these scans? For my other scans, sometimes the differences in intensity are very subtle. For example, I have one scan where the contrast between the GM and WM are more apparent at one time point vs. the other time point. In another example, the thalamus looks a bit darker at time 1 vs. time 2. Again these differences are very subtle and only noticeable if you are looking for them. I am just wondering at what point do these differences become problematic? I should also note that sometimes these differences are not readily apparent in the original T1 scan. Thank you again for your help. Best, Tamara

2 1

Defining labels and Gordon 2014 annotation file
by Ladan Shahshahani 27 Dec '16

27 Dec '16

Dear experts, I want to use ROIs from Power et al. 2011 paper (Functional network organization of the human brain). An excel file is provided with the center coordinates. I wonder if it's possible to use this file to automatically create parcels. Is there any way of getting Gordon's 2014 parcellation annotation file in fsaverage space? Best regards, Ladan

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mri_cvs_register
by N Saf 26 Dec '16

26 Dec '16

Dear Freesurfers, I try to register my subject with cvs atlas in mni space I use this command mri_cvs_register --mov subject.nii --mni I got this error: Using m3z type morph files. amir : at least one mean and/or Gaussian curvature file is missing (.H, .K) /home/nazanin/freesurfer/subjects/amir/surf: No such file or directory. should I first do some processing with freesurfer for my subject and then use this command ??? and if so what is the minimum processing I should run before using mri_cvs_register command?I saw a similar question in mailing list but I did not find the answer ,in advance I apologize if it can be repetitive.another question is that if it's possible to register my subject with the probability map of cvs atlas ?? Best Regards, Nazanin

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From SUMA Dset file to Freesurfer file( overlay an gii file on fsaverage brain)
by Fatemeh.Molaei-Vaneghi 23 Dec '16

23 Dec '16

Dear FreeSurfers, I am doing some thing similar to the post from Zhiwei (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40540.html) I want to map visual topographic probabilistic maps (http://scholar.princeton.edu/napl/resources) from Princeton university onto the fsaverage. After converting these maps from SUAM 1d.dset format to FreeSurfer .gii format, I tried to map them onto fsaverage6 as annotation files in tksurfer. The following is the error message I got in tksurfer: mrisReadGIFTIfile: malformed data array [0] in file /Volume/DATA/Studies/FS/SubjectData/fsaverage6/maxprob_surf_lh.gii: num_vertices=198812 num_cols=1 expected nvertices=40962, num_cols=1 The probabilistic map (maxprob_surf_lh.gii) is composed of two columns, the first one being node index ranging from 1 to 198812 and the second one being node value (nodes/vertices that belong to a certain surface ROI get a certain value, the rest of the nodes get the value of zero in the second column). These maps have been created in icosahedron surface space (using SUMA's MapIcosahedron -ld 141) using Buckner40 dataset. Taking into account that fsaverage is also derived from this dataset I don't understand why there is no vertex correspondence between these two surface files. One should note that these files are 1d vectors, and therefore, no auxiliary information such as label and parent surface, etc is preserved in these files. With this intro, my question is how project these maps onto the fsaverage so they can be easily visualised in FreeSurfer? Best, Fatemeh Molaeii Max Planck Institute for Biological Cybernetics Spemannstr. 41 72076 Tübingen Germany

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Regarding: Segmentation violation detected (FS version dev6)
by Dr Sampada Sinha 23 Dec '16

23 Dec '16

Dear freesurfer experts, I am trying to so the brainstem segmentation with freesurfer version *freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae. *I incorporated the MCR in the fs dev directory. When I run the command recon-all -s foo -brainstem-structures. I am getting the following error: MATLAB is exiting because of fatal error: /usr/local/freesurfer/bin/run_SegmentSubject.sh: line 38: 10488 Killed: 9 "${exe_dir}"/segmentSubject.app/Contents/MacOS/segmentSubject $args. Will you please let me know I do I fix this? My subjects were processed with: freesurfer-Linux-centos6_x86_64-dev-20160211. Presently I am working with freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae. I am incorporating the matlab crash dump file with mail. Your help will be greatly appreciated. -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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Freesurfer December 2016