Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

overlaying sig.mgh onto normalized individual brains
by Catherine Wan 06 Mar '12

06 Mar '12

Dear Freesurfer-list, Please excuse me if this question sounds very simple. I work with lesion brains and I want to overlay the group level result (sig.mgh) onto individual brains to check whether it covers the lesion (which we don't want). I first used mri_surf2vol to convert sig.mgh to a volume. I then mri_vol2vol to normalize the individual T1.mgz to the fsaverage T1, but when I overlaid the sig.mgz onto the normalized T1, it didn't look well-registered (see attached jpeg). However, when I overlaid the same sig.mgh onto the fsaverage T1, it looked completely fine. I'm wondering if anyone could tell me how to better register the individual T1 so I can check whether the individual lesion overlaps with the group level results? Some of the brains went through tkregister2 and the segmentation looked fine afterwards. Any guidance would be much appreciated! Regards, Catherine

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PhD / Post-Doctoral position – Neuroimaging of language and audition, University of Geneva
by Narly GOLESTANI 06 Mar '12

06 Mar '12

PhD / Post-Doctoral position – Neuroimaging of language and audition, University of Geneva ------------------------------------------------------------------------------------------------------------- Applications are invited at the PhD or at the Post-Doctoral level at the Department of Clinical Neuroscience at the University of Geneva in Switzerland, under the supervision of Professor Narly Golestani. Projects will include developing new methods to analyze aspects of brain morphology using structural MRI, and applying these in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and experience with analysis of structural MRI data and with programming are highly desirable. Applicants should have a strong interest in neuroscience and ideally also in research on language and audition. The position can start as early as April 1st 2012, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani@unige.ch(https://webmail.unige.ch/horde/imp/message.php?index=6)). Applications including a CV, a statement of research interests, and the names and full contact details of two referees should be sent to: Narly.Golestani@unige.ch(https://webmail.unige.ch/horde/imp/message.php?index=6).

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Research scientist in MRI imaging – three-year contract available immediately
by Frédéric Andersson 06 Mar '12

06 Mar '12

Research scientist in MRI imaging – three-year contract available immediately The Physiology of reproduction and behaviour combined research unit at the INRA centre of Tours is recruiting a research scientist specialised in MRI for its imaging platform. This internationally recognised facility for imaging of medium sized domestic animals will be equipped with a 3T MRI, an X-ray scanner and an ultrasound echography machine. The facility employs seven staff including a veterinary surgeon, and technical staff to prepare the animals, anaesthetise, and provide pre- and post-operative care. The recruited scientist will carry out MRI imaging experimentations on different domestic animal models (pig, sheep, goat and rabbit). The main areas of investigation are the abdomen and the central nervous system. The successful candidate will have contact with many different people involved in the protocols of the different research teams. Within the department he/ she will be in charge of developing and adapting the imaging protocols (MRI) for domestic animals. The job will involve analysing the imaging needs of the different research teams and developing innovative and appropriate methodologies to meet these needs. The recruited scientist will take part in training and teaching sessions. He/ she will be required to integrate the national and European medical imaging networks, and to draw up close links with the imaging teams from the Medical School and Teaching Hospital of Tours, where these imaging techniques are developed on clinical models, integrating the network of skilled staff for these structures. This position does not involve any specific constraints. The job will involve: • Studying the needs related to the research aims of resident and partner teams; • Proposing suitable imaging strategies (from acquisition to analysis) for the research problematics of these teams, in terms of acquisition protocol, sequences and parameters; • Optimising the existing MRI acquisition procedures for humans for use with animal models; • Developing original MRI sequences corresponding to the scientific problematics of the users; • Ensuring technological intelligence in the field of MRI sequences; • Promoting original developments within the scientific community of MRI “methodologists”; • Training users in original acquisition procedures developed for their needs; • Liaising with the manufacturers of the MRI system for software updates, upgrading and maintenance; • Organising and checking preventive maintenance and repairs in liaison with the manufacturers; • Carrying out quality checks on acquisitions; • Coordinating use of the system; • Overseeing measurement taking, interpretation of results and their validation for scientific analysis in compliance with the quality system; • Managing the technical resources allocated to a research project or protocol; • Presenting, disseminating and promoting achievements and results. Taking part in teaching both in higher and continuing education, contributing to training of students through research, training and advising users on the deployment of the experimental systems; • Managing technical documents relating to the domain; • Taking part in the research projects of the Unit’s teams. Skills required: - In-depth knowledge of NMR physics, and in vivo NMR imaging and spectroscopy; - In-depth knowledge of MRI instrumentation and sequence programming; - Ability to analyse images and process signals; - Interest in programming; - Good relational skills in a multi-displinary context; - An operational level of scientific and technical English (good oral and written comprehension); - Skills in X-ray imaging would also an advantage; - Basic knowledge of physiology would be an advantage. Know-How - Quality control; - Technological intelligence/ literature search; - Scientific promotion; - Organisational management; - Ability to integrate various elements relating to different technological fields (magnetism, computing, electronics, etc); - Know-how in experimental imaging of large animals would be an advantage. Required training/ professional experience - PhD in biophysics, physics, image analysis or signal processing, and/or an engineering degree in the same fields with skills in nuclear magnetic resonance (NMR); - Experience in NMR sequence programming for in vivo imaging; - A qualification in animal experimentation is recommended. - Post-doc professional experience is highly recommended. Personal qualities: Capacités personnelles : - Good human skills and ability to work in a team in a multi-disciplinary context; - Good communication and organisational skills; - Good animal skills; - Thorough. Contact: Send your CV and cover letter to: Yves Tillet, INRA-PRC, UMR7247, Directeur de l'FR135 "Imagerie Fonctionnelle", 37380 Nouzilly mail : yves.tillet(a)tours.inra.fr Tel : 02 47 42 77 98 (secretary)

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About recon-all
by bowang21＠mail.ustc.edu.cn 06 Mar '12

06 Mar '12

Dear all I just want to ask a sample question.What's the best number of the parameter of 'recon-all' , -i invol1 -i invol2.That is, how many slices should we use?If the invol1 is the fist slice of the fMRI series or any one of the data? Yours

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mri_cvs_register on a 64-bit Mac crash PETSC ERROR
by Rey Ramirez 06 Mar '12

06 Mar '12

Dear colleagues, especially Lilla Zollei, I am trying to run mri_cvs_register on a 64-bit Mac but it crashes at the same place where other people had reported a problem. I tried updating mri_cvs_register from ftp as recommended in: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018786.html but that didn't help. The problem seems to be the exact same problem mentioned on this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-December/021457… I paste a small chunk of the log below at the point the PETSC ERROR occurs. I attach the whole log file. Has anyone come up with a solution? Thanks so much for your help, Rey ... setting bc 51.75 25.0698 42.9884 -> 0 0 0 instead 51.76 25.0798 42.9984 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 77063 Total BCs = 527338 no-eqs = 209160 surf2vol(51421) malloc: *** mmap(size=251830272) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 251828644! ... -- Rey R. Ramírez, Ph.D. MEG Brain Imaging Center Institute for Learning & Brain Sciences Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 e-mail: rrramir(a)uw.edu Tel: (206) 543-6484 Fax: (206) 221-6472 Cell: (619) 709-3590

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Freeview NIH Color Map
by Blazey, Tyler 05 Mar '12

05 Mar '12

Hi, Is there any way to prevent the NIH color map in Freeview from displaying values higher than the max as black? I can only seem to find this option for the Heat color map. Thanks for any help, -Tyler ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). 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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(no subject)
by Ryan 05 Mar '12

05 Mar '12

Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command "recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz" and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting output onto subject 7107-46-tp1. processing subject lh.EC_average... MRISread(/media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.r$ Too many levels of symbolic links Linux mriserver.archlab 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 7107-46-tp1 exited with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan

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mri_vol2surf error writing to nifti volume
by Tina Jeon 05 Mar '12

05 Mar '12

Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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controls points in 5.1
by Chris Hyatt 05 Mar '12

05 Mar '12

Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0. Would anyone know if this flag exists and how to use it? Thanks, Chris Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800 Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce

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pwd: permission denied
by Marcel Zwiers 05 Mar '12

05 Mar '12

Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz -autorecon1 [..] However, if I run the same command on the same file, except that this file is now located in a directory of a colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 pwd: cannot open directory `../..': Permission denied /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied [..] >From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause and hope you have any ideas here. Cheers, Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands

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Freesurfer March 2012