Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

average_thickness&mris_anatomical_stats
by Liukarl 22 Mar '11

22 Mar '11

Hello, Freesurfer experts: I am using the mris_anatomical_stats to extract the average cortical thickness: mris_anatomical_stats -l lh.cortex.label -f subject1.txt subject1 lh the output is number of vertices = 127190 total surface area = 84246 mm^2 total gray matter volume = 257279 mm^3 average cortical thickness = 2.628 mm +- 0.698 mm average integrated rectified mean curvature = 0.158 average integrated rectified Gaussian curvature = 0.146 folding index = 6266 intrinsic curvature index = 403.9 My question is whether the average cortical thickness here is from white matter surface or pial surface? How can I get the pial surface average thickness? Our goal is to use average cortical thickness as a covariate to examine the possible local thickness difference, like in the prefrontal lobe. Which average cortical thickness, pial or white, is a better fit in our case? Thanks in advance Karl

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Re: [Freesurfer] 2x2x2 design
by Gabriel Go.Es. 22 Mar '11

22 Mar '11

Just ideas I had about how to set the contrast for ANOVA, but not sure if any of them is valid. Gabriel > Date: Fri, 18 Mar 2011 13:57:31 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: gabriellbk(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 2x2x2 design > > Gabriel, what are options 1 and 2 supposed to represent? > doug > > Gabriel Go.Es. wrote: > > > > Dear Freesurfer experts, > > I'm wondering how to set a 2x2x2 anova > > > > (diagnosis)x(gender)x(apoe) > > > > g1MaleE4 > > g1MalenoE4 > > g1FemaleE4 > > g1FemalenoE4 > > g2MaleE4 > > g2MalenoE4 > > g2FemaleE4 > > g2FemalenoE4 > > > > option 1 > > [1 1 -1 -1 0 0 0 0] > > [1 1 0 0 -1 -1 0 0] > > [1 1 0 0 0 0 -1 -1] /2 > > > > option 2 > > [1 1 1 1 -1 -1 -1 -1] > > [1 1 -1 -1 1 1 -1 -1] > > [1 -1 1 -1 1 -1 1 > > -1] /4 > > > > > > And really have no idea about the interections between factors. Could > > you tell me for example how to evaluate the diagnosis x gender > > interaction effect and the interaction among the three factors > > (diagnosis x gender x apoe). > > > > Bests regards, > > Gabriel > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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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tkmedit undo volume?
by Nugent, Allison C. (NIH/NIMH) [E] 22 Mar '11

22 Mar '11

Hi - I'm doing manual edits in tkmedit. In the tkmedit "working with data" page on the wiki, it states that there are three ways to "undo", one taking advantage of the "undo volume." The instructions say to select View->Undoable voxels, then use the shift key and mouse button 2 with the edit voxel tool active, the voxels will be returned to their original values. I have the latest version of freesurfer, and there is no "undoable voxels" in the view menu. I can view edited voxels. However, nothing is undone when I hold the shift key. Under edit, however, there is an option to "clear undo volume" which makes me think that the undo volume still exists. Is this still an option for editing? Thanks, Allison Allison Nugent, PhD MRI Physicist Section on Neuroimaging in Mood Disorders Experimental Therapeutics and Pathophysiology Branch NIMH/NIH/DHHS Ph. 301-451-8863 nugenta(a)mail.nih.gov

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[New release] - iSurf Brainview 2.1.0
by Pedro Paulo de Magalhães Oliveira Junior 22 Mar '11

22 Mar '11

Today it was released a new major upgrade of iSurf Brainview. (2.1.0) New features: - New Atlas: Chistophe Destrieux 2009 Atlas - Improved Interface - Retina Display - iOS 4.3 As usual suggestions are welcome. Upcoming features will include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr.

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Content of .tif files
by Anderson Winkler 21 Mar '11

21 Mar '11

Hi all, The .tif files (templates) contain 9 pages each, which seem to be organized as 3+3+3. I think I understand that they are equirectangular projections of the latitude/longitude of curvature and sulcal depth, is this correct? But what exactly each of these 9 frames contain? Thanks! Anderson

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using multiple processors with freesurfer?
by jim kroger 20 Mar '11

20 Mar '11

Hello, I just downloaded freesurfer and am processing some of my data. I am using an 8 core machine, but I'm guessing freesurfer is using only one processor. Can you point me to information about taking advantage of multi cores when using freesurfer, if that is possible? Many thanks, Jim Kroger NMSU Psychology Los Alamos National Labs -- Cell: 575-571-8274 Email: jkk251(a)gmail.com Email to my other, work address will still reach me.

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recon-all parallel execution of hemi stages
by Satrajit Ghosh 20 Mar '11

20 Mar '11

it seems we could run lh/rh processing stages of recon-all in parallel. however, i think they will write to the same log files. is there a way to specify a different log-file prefix? are there any other common files that these hemisphere based operations write to? concurrent reading i'm assuming is ok. cheers, satra

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Watershed treshold and amygdala volume
by Hendrikx, A.A.E.M. (Anne) 20 Mar '11

20 Mar '11

Dear all, We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following: We are wondering why the amygdala volume changes, after changing the watershed threshold. Besides, if we should nog change the ws-treshold, but manually remove remaining skull, the amygdala volume will not change. We don't understand this. Can anyone explane this to us? And besides, what consequences are there for the accuracy of the calculations? Best wishes, Anne Hendrikx

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Able to load surfaces but not *.mgz files in MATLAB...
by Eggebrecht, Adam 18 Mar '11

18 Mar '11

Hello, I have installed FreeSurfer on a Linux box and everything works great. However, our lab does most all of our processing in MATLAB in a Windows XP-64 platform. Within MATLAB, I am able to import the files existing within the /surf/ folder to work with and visualize the meshes. However, I am unable to load in any of the *.mgz files within the /mri/ folder. I have attempted to use the load_mgh.m and MRIread.m commands. The error returned is the following: The system cannot find the path specified. ERROR: could not open /tmp/tmp5897063.mgh for reading ERROR: loading mri/wm.mgz as MGH The load_mgh.m program is failing between lines 61 and 76. I don't know how your code is compressed, so I can't create a work around for this specific issue. Is this program only useful on a MAC or unix-based system? Is there another way to load in the compressed files into a Windows-based MATLAB? I have searched the relevant help threads, but have not found an answer to this specific problem. Many thanks for your assistance! Cheers, Adam Adam T. Eggebrecht, Ph.D. Dept. of Radiology Washington University School of Medicine St. Louis, MO 314-362-6942 The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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monkey brain problem
by Yang Liu 18 Mar '11

18 Mar '11

Hi surfers, We met a problem when processing a monkey's anatomical brain. We got a very good white matter segmentation (wm.mgz) by manually editing the automatic segmentation. After recon-all, we found that at some regions, the yellow surface won't follow the wm.mgz. It is strange because the wm.mgz at these regions are very well defined and smooth. I would expect that the main surface would follow the wm.mgz tightly and smoothly. You can see the problem from the images I attached. These are coronal and horizontal views of one region. Actually I posted the same type of problem for the other monkey's brain in January. We have solved the problem by filling all the ventricles and improving the smoothness of wm.mgz. However, we tried all methods that we learnt from the previous monkey on the second monkey, but all failed. I am curious about how the main (yellow) surface is generated. Is it purelly reconstructed from wm.mgz, or it also need brainmask.mgz? I also edited the brainmask.mgz by darkening the gray matter surrounding the problematic regions, but it didn't work out either. I think this problem might be quite common for the monkey community, because we met it on both of our monkeys. Thanks, Yang Liu

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Freesurfer March 2011