Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Re: [Freesurfer] freesurfer trouble with FTLD subjects
by Adam Mezher 28 Oct '14

28 Oct '14

Hi Bruce, I performed both cp and wm edits and was able to fix most of the subjects in the meantime. I’ll still see if I can get it ftp’d over to you guys to take a look for future reference. thanks! Adam Hi Adam it's impossible to say without seeing some examples. If you upload a problematic subject (the entire subject directory from recon-all) we will take a look cheers Bruce On Wed, 22 Oct 2014, Adam Mezher wrote: > Hi All, > I'm running a number of subjects who have FTLD and their > surfarce/parcellation outputs are quite poor (especially in the frontal lobe > obviously). Are there any expert commands that can be used to attempt to fix > this issue without having to do individual edits? Most of the subjects have > underestimations in most frontal gyri and insula. > > Thanks a lot, > Adam > > Adam Mezher > USC Imaging Genetics Center > Marina Del Rey, CA > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
by Lars M. Rimol 28 Oct '14

28 Oct '14

Hi Doug, For some reason, I no longer get an e-mail when you respond to my questions on the mailinglist, so until today I only saw the first response to this question (from Bruce). Anyway, I get your point about smoothing and clusters but I guess showing a continuous cortical map with vertex values should be ok, right? The map itself is rather smooth and it's impossible to see the individual vertex in the figure, so we're basically saying "this region generally has about 0.8% reduction" (for instance). Also, how much precision can I assume here? 0.004 mm^2 is not very much. These changes are apparently very consistent across subjects since most of the cortex shows significant change. But what if we find very consistent changes that are on the order of 0.000001 mm², which therefore become statistically significant? Is that beyond our level of precision here? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway

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Overlay transparency
by Roberta Santoro 27 Oct '14

27 Oct '14

Dear all, I have selected some vertices that I would like to overlay on an inflated surface and I would like the overlay to have opacity<1 such that I can see the curvature underneath. I am using a script for doing this and everything works, but the opacity doesn’t change when I use the command sclv_set_overlay_alpha 0.5. Does anyone know how to fix this problem? Thanks a lot Roberta

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ICV for adolescent and young adult in longitudinal stream
by Knut J Bjuland 27 Oct '14

27 Oct '14

Dear FreeSurfer export, I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points? Best regards, Knut Jørgen Bjuland PhD candidate NTNU Trondheim

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Appropriate levels of surface smoothing
by Kirstie Whitaker 27 Oct '14

27 Oct '14

Hi everyone, Firstly - thank you for the excellent tools. This year has been my first foray into surfaced based analysis and I'm enjoying it very much. I don't currently have a gut instinct for an appropriate level of surface smoothing. I'm sure that can't be easily answered but would a range of, say, 3 to 5mm sound good? Or more like 10 to 15mm? Currently I'm considering cortical thickness analyses, but I may extend into functional analyses in the future. If there are any references that you can recommend I'd appreciate that very much. Best wishes Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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template to dicoms
by Linda Douw 27 Oct '14

27 Oct '14

Dear freesurfers, I have a bit of a strange question: does anyone know a way to write a template T1 brain (for instance fsaverage or MNI152) to dicom files? I have some very old software that only takes dicoms and it's the only software I can use to replicate previous findings, but obviously going from a template to dicoms is not that easy. I'd appreciate any tips! -- Linda Douw, Ph.D. Branco Weiss fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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accepting students cognitive neuroscience program 2015
by Anthony Dick 27 Oct '14

27 Oct '14

The Florida International University Cognitive Neuroscience Program in Psychology is accepting graduate students for Fall 2015. Please see the attached flyer for more information. -- Anthony Steven Dick, Ph.D. Assistant 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: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org

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Parenchyma over CSF rartio
by Mahmoud 27 Oct '14

27 Oct '14

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud

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Error when launching qdec
by Claire Morley 27 Oct '14

27 Oct '14

Hello Freesurfer Community, I am now having issues getting qdec to launch as well. The qdec window pops up momentarily but then disappears. This is the error message I get: error: xp_attach_gl_context returned: 2 X Error of failed request: 0 Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 26 (X_GLXMakeContextCurrent) Serial number of failed request: 1157 Current serial number in output stream: 1157 Could XQuartz somehow be the problem? I am now running XQuartz 2.7.5 on my Mac that`s in Mavericks. Thank you so much again for all of your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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better accuracy of FreeSurfer compared to SPM?
by marisa.poeschl＠web.de 27 Oct '14

27 Oct '14

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Freesurfer October 2014