Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

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

2 1

[FreeSurfer] aparc.a2009s.stats, MeanCurv, GausCurv
by Hanbyul Cho 22 Sep '16

22 Sep '16

Dear FreeSurfer Team, I heard that the processed subjects/stats/?h.aparc.a2009s.stats included the integrated rectified mean curvature value (MeanCurv) and integrated rectified Gaussian curvature value (GausCurv). I wonder that whether the integrated rectified curvature values are about pial surface or white matter surface. Thank you. Best wishes, Han

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freesurfer longitudinal data
by Gabor Perlaki 22 Sep '16

22 Sep '16

Dear all, Is it possible to get simple ROI data (such as aseg.stats or aparc.stats in case of cross-sectional analysis) as the result of the longitudinal analysis, which can be further analyzed by SPSS? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

2 1

cluster feature extraction from qdec output
by Damien MARIE 22 Sep '16

22 Sep '16

Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispheric surface area as nuisance factors, so I would like to get the feature residuals after the removal of the covariate effects. I am sorry, I saw several posts about that but for me it’s not completely clear what command line I should use to get tables for this… Thank you and best, Damien

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optseq2 question
by Yoed Kenett 21 Sep '16

21 Sep '16

hello i am trying to use optseq2 to design a study. I have a new mac book pro with El Capitan installed. I have tried downloading all different optseq2 versions but each time when i try to run it through the terminal i get the same exact error: -bash: optseq2: command not found what am i doing wrong here? which version should i use and how do i get it to work? thanks so much Yoed

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