Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
by Fengji Geng 14 Jan '16

14 Jan '16

Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! --------------------------------------------------------------------------------- Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <568ABBFC.5000702(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! ----- Fengji

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Visualizing GLM analysis error
by Myers, Peter 14 Jan '16

14 Jan '16

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Cortical reconstruction
by Mohamed Ali Bahri 14 Jan '16

14 Jan '16

Dear Freesurfer Experts, I am wondering if the cortical reconstruction is possible for the quantitative mri images (R1, MT, PD...) obtained with the multiparameter sequences . If yes which image should i use? Many thanks in advance, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

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Postdoctoral position available, Paderborn (Germany)
by Claus Reinsberger 14 Jan '16

14 Jan '16

The Institute of Sports Medicine at the University of Paderborn invites applications for a full-time Postdoctoral Position to conduct, process and analyze EEG and other neuroimaging data in the context of sports and exercise. The primary responsibility of this position includes developing novel processing and statistical analysis methods, specifically for analyzing properties and dynamics of resting state networks, in dependence of various demands and states of fatigue in sports and exercise. The start date can be immediate and the position is scheduled for three years. Applicants are expected to have finished their PhD in biomedical engineering, Computer Science, Medical Physics, Neuroscience or related disciplines with a track record of relevant publications. The project requires experience with mathematical modeling and strong programming skills in C/C++ and Matlab/Python. Proficiency with EEG analyses is essential, experience with image registration and other statistical methods for neuroimaging are welcome. We are looking for a personality with the ability to think independently and work collaboratively, paired with high communication skills and high proficiency with English language. Postdocs will have the opportunity to strengthen their scientific and professional qualifications. The teaching responsibilities amount four semester periods per week. The Institute of Sports Medicine at the University of Paderborn is the first sports medicine program in Germany under neurological leadership with a strong focus on neurophysiology in health and elite level sports. The posted position will further the unique neurophysiological profile within the new field of applied neurosciences in sports and exercise. Applications from women are particularly welcome and, in case of equal qualifications and experiences, will receive preferential treatment according to the North Rhine-Westphalian Equal Opportunities Act (LGG), unless there are preponderant reasons to give preference to another applicant. Applications from disabled people with appropriate suitability are explicitly welcome. This also applies to people with equal opportunities in accordance with the German social law SGB IX. To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: Reinsberger(a)sportmed.upb.de <mailto:Reinsberger@sportmed.upb.de> Claus Reinsberger, MD PhD Department of Exercise and Health Institute of Sports Medicine University of Paderborn Warburger Str. 100 33098 Paderborn, Germany

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Re: [Freesurfer] X-inversion for b-vectors extracted via mri_convert?
by Anastasia Yendiki 13 Jan '16

13 Jan '16

Hi Emad - I wouldn't do tractography to check the gradient vectors. All you need is to look at are the principal eigenvectors of the tensors (dmri/dtifit_V1.nii.gz), displayed as lines (not just RGB map, that's less informative). If, for example, the z coordinates need to be inverted, then the eigenvectors will look wrong in the coronal and sagittal view (the two views that involve the z dimension). Hope this helps, a.y On Mon, 4 Jan 2016, Emad Ahmadi wrote: > Hi FreeSurfer Experts, > > Happy New Year! > > I am using mri_convert to extract b vectors (bvecs) from diffusion images obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. The shape of the reconstructed pathways are odd, so I wanted to check if the extracted bvecs are correct. > > To check if the extracted bvecs are correct, I put them in Diffusion Toolkit, did deterministic tractography, and checked the shape of the extracted nerve fibers. In the attached ppt file, the first three slides show the shape of the extracted fibers. You can see that they don’t look right. > > Then I inverted the X components of the extracted bvecs, and did the tractography again. The last three slides show the result, which look right now. > > I had the same experience with dcm2nii tool, where I had to invert the Z component of the extracted bvecs. Just wanted to see if others have hit the same problem and confirm that I should invert the X component of the bvecs extracted via mri_convert. > > I hope a wonderful new year for everyone! > Emad > > Emad Ahmadi, MD > ----------------------------------------------- > Research Fellow in Radiology > Massachusetts General Hospital > Harvard Medical School > > 25 New Chardon Street, Suite 400 > Boston, MA 02114 > Tel: 617 726 5237 > Email: emad(a)nmr.mgh.harvard.edu > >

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Trac-all -path Segmentation error
by Katherine Damme 13 Jan '16

13 Jan '16

Hello Everyone! It looks as though my prep and bedp stages completed properly, but the prep stage ends in a segmentation errror. See attached and let me know your thoughts. I would prefer not to have to redo all steps if possible! Thank you!

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Cortical thickness parcellates
by John Anderson 13 Jan '16

13 Jan '16

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Error with pial surface and white matter surface boundaries
by Marissa Pifer 13 Jan '16

13 Jan '16

Hi Freesurfers In processing data in FS I've run into a problem that I haven't seen before. I've attached the photos for your reference. The scan is a base template (made up of 3 individual scans). The pial surface boundary and the white matter boundary look to be correct, but it is as if they are just shifted slightly to the right. I looked at the individual scans but it wasn't like this on any of those. I'm not sure why this would happen or how to fix it. If you have any suggestions please let me know. Thanks in advance, Marissa

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registration errors in longitudinal analysis
by Lara Foland-Ross 13 Jan '16

13 Jan '16

Dear Freesurfer experts, I am working on a longitudinal analysis of cortical structure and am experiencing some errors with registration. I have 3 timepoints for each participant: time 1: age 2 time 2: age 5 time 3: age 10 Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner. Despite the age range and scanner difference, the registrations in the longitudinal pipeline (I'm using version 5.3) are performing relatively well. However, in comparing the LONG outputs slice by slice, it appears that in a majority of my subjects, there are some minor mismatches in brain anatomy. An example is attached here (minor_reg_error.jpg). In other instances, there are more substantial registration errors. Again, example attached here (major_reg_error.jpg). My question is how much mismatch is acceptable? And how can I go about fixing poor registrations in subjects who have significant errors in alignment? Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 13 Jan '16

13 Jan '16

Dear Bruce, thanks for answering. The recon-all command lines we use is: recon-all -s subjectID -i /data/subjectID.nii.gz recon-all -s subjectID -all The files we used are 1) DICOM files 2) nii.gz files, but standard oriented and cut 3) nii.gz files When we look at the output pictures, they look different (see attached files) Greetings, Susanne ______________________________________ Susanne Schell, Dipl.-Psych. Sektion Störungen der Persönlichkeitsentwicklung Klinik für Kinder- und Jugendpsychiatrie Universitätsklinikum Heidelberg Tel: (+49) - (0)6221-56 35135 e-mail: susanne.schell(a)med.uni-heidelberg.de<mailto:susanne.schell@med.uni-heidelberg.de>

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Freesurfer January 2016