Freesurfer

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30099 discussions

Corpus Callosum segmentation
by Nathaniel Lucena 28 Oct '14

28 Oct '14

Is the corpus callosum segmentation based on the Hofer and Frahm functional parcellation, a mathematical formula, or, as listed on the website, 5 equal subdivision roughly along the long axis? What is the preferred citation for this? Thanks.

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GI analysis of single subject
by Maria Holland 28 Oct '14

28 Oct '14

Hi all, I'm trying to get gyrification information about a single subject. I've run the -localGI process but I have a few questions about the results: 1. When I try to plot the smoothed out pial surface over the brainmask in freeview, I use the command freeview -v subject/mri/brainmask.mgz -f subject/surf/lh.pial-outer-smoothed but it appears to be an inflated surface of some sort. It doesn't hug the contours of the brain mask as I expected (or as shown in the top image here: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) How can I see that surface? 2. I see very little variation in the local GI. I'm wondering if the third image in the link above is typical, and also how to get the blue to red color scale as shown? I can only get red to yellow, which doesn't show as much variation. 3. There is information on how to run analysis on a group of subjects, but I'm wondering if it's possible to get numerical data on a single subject. For instance: average GI in a given ROI, global GI, distribution (min, max, std dev, etc.). If nothing else, can I get the numerical values for each vertex? Thanks for your help! ~ Maria Holland Stanford University

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Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
by Smith, Michael 28 Oct '14

28 Oct '14

I guess I'm not entirely sure how to do that? Are there any tutorials on how to extract an ROI from the aparc.stats file? -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 22, 2014 4:21 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: > Hello Freesurfer's > > I am trying to look at the cortical thickness for a specific ROI on > the cortical surface (Primary Auditory Cortex: transverse temporal > gyri). I found a specific tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) > however the tutorial assumes I already have an ROI mask created. I was > wondering if anyone had any tips on creating an ROI for the cortical > surface from the parcellation/annotation files. I know you can > "hand-draw" ROI's in tkmedit or freeview but I would prefer something > less subjective that doesn't rely on my untrained eye and unsteady > hand! Thanks in advance. > > Best, > > Michael S. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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] 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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