Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Regional White Matter Hypointensity Volumes
by Bharadwaj, Pradyumna - (prad) 26 Sep '16

26 Sep '16

Hello Freesurfers, I am interested in obtaining the regional volumes of white matter hypointensities. What volume would I use a reference for obtaining the 'regions' ? and what commands would I need to use to obtain these regional volumes ? ?If there isn't an appropriate white matter volume that can be used as a reference, then is there a way to divide a subject's brain image or white matter volume image into say 8 equal quadrants, which can then be used as masks to obtain regional WMH volume in these quadrants? Thanks, -Prad

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Re: [Freesurfer] Software License for Industry
by zkaufman＠nmr.mgh.harvard.edu 26 Sep '16

26 Sep '16

The FreeSurfer Software License Agreement does not contain any language explicitly or implicitly preventing commercial usage, however I will highlight the following text from the License Agreement: "Any commercialization of the Software is at the sole risk of the party or parties engaged in such commercialization In short, commercial entities seeking to make use of FreeSurfer should seek their own legal council on the interpretation of the license for their specific circumstance. -Zeke > Dear FS experts > > I have one concern regarding the license and the Freesurfer usage on > industry. > > We are setting up a start-up specialized with the analysis of brain MRI > and > we are interested on using FreeSurfer package as our main neuroimaging > tool, due to the large amount of utilities it provides. > > After reading carefully the Software License provided here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is > not clear for me if we could use yours software to provide a service to an > external organisation/customer for which payment will be received. > > Could someone provide some insight on this issue? > > Bests, > Joss. >

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Software License for Industry
by Josseppe Gonsales 26 Sep '16

26 Sep '16

Dear FS experts I have one concern regarding the license and the Freesurfer usage on industry. We are setting up a start-up specialized with the analysis of brain MRI and we are interested on using FreeSurfer package as our main neuroimaging tool, due to the large amount of utilities it provides. After reading carefully the Software License provided here ( https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is not clear for me if we could use yours software to provide a service to an external organisation/customer for which payment will be received. Could someone provide some insight on this issue? Bests, Joss.

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Postdoctoral Positions -- Baby Brain Connectome
by gangli 26 Sep '16

26 Sep '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic development of brain structure, function and connectivity during critical early postnatal stages, via computational analysis of high-quality multimodal neuroimaging data acquired by UNC/UMN Baby Connectome Project. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The postdoctoral candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu)

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White matter editing using control points
by Jannike Ausland 26 Sep '16

26 Sep '16

Hi, I am having some trouble with white matter editing using control points. I am placing control points in white matter with intensity <110, and I find that it seems to have different effects in different slices/subjects, which makes it hard to develop a general standard for control point editing. Additionally, the curve outlining white matter is often less correct after control point edit, also some distance away from where control points are added. So, how does Freesurfer interpret control points and what exactly happens when control points are added? How does the number of control points used and the intensity of the voxels in which the control points are placed determine the outcome? Thanks, Jannike

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two postdoctoral fellowships; Florida International University, Miami, FL
by Anthony Dick 25 Sep '16

25 Sep '16

Please distribute! http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/ -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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license.txt?
by Trisanna Sprung-Much 24 Sep '16

24 Sep '16

Hi there I am installing Freesurfer on a Mac for the workshop next week and I cannot seem to get a license.txt because the page is no longer is accessible. However, it seems to be running fine without this file. Thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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avoiding FSL when using T2pial
by Satrajit Ghosh 24 Sep '16

24 Sep '16

hi doug, without hacking recon-all is there a way to avoid using FSL when using the T2pial flag? cheers, satra #@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log Sat Sep 24 08:42:35 UTC 2016 setenv SUBJECTS_DIR /subjects cd /subjects/sub-01/scripts /opt2/freesurfer/bin/bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64 GNU/Linux FREESURFER_HOME /opt2/freesurfer mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /subjects/sub-01/mri/orig/T2raw.mgz... TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0675638, -0.9838, -0.166052) j_ras = (0.119725, -0.173224, 0.977578) k_ras = (0.990505, -0.0461684, -0.129489) writing to /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii... fslregister --s sub-01 --mov /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii --reg /subjects/sub-01/mri/transforms/tmp.bbregister.4836/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /subjects/sub-01/mri/transforms/tmp.bbregister.4836/fslregister --dof 6 --fsvol brainmask.mgz ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation

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freeview display problem
by KALEY E ELLIS 23 Sep '16

23 Sep '16

Hello FreeSurfer Developers, I am attempting to open freeview to view the brainmask on a subject in our study. Everything looks normal, except there is no image displayed (see attachment). Could you please let me know how I can fix this? Thank you, Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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Question regarding mri_convert
by Tamara Tavares 23 Sep '16

23 Sep '16

Hi All, I have been using the following command line to convert my dcm/IMA files into a nii files. mri_convert -it dicom xxxxx.dcm xxxx.nii (where xxxx are the name of my files) I realized now that I did not specify the output file type (-ot nii) before the file name. Is this a big concern or are these files still good to use on Freesurfer? In the past, I have toggled between the original volume and the new nii file and everything looks the same. Also, when I have ran it through the standard Freesurfer processing stream, it seems to work fine and there are no errors. Thank you in advance for your help Best, Tamara

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Freesurfer September 2016