Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

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by Antoine Leflon 04 May '10

04 May '10

hello all , I managed to run recon-all fully and I got a table with the following colums : number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index "" structure name the 9th column has no name (the one I've called "") Can Somebody explain or tell me what does this column refers to ? thanks , Antoine

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Submitting Files for Review
by Stefan Du Plessis 04 May '10

04 May '10

Dear All I want to send a file will an example of the segmentation of the Pallidum, as discussed previously, which I want refined in general for my OCD project. Do you generally want only the subject file folder with contents, or the mgz file only? Also when uploading from South Africa, what is the best place for me to upload and how? Also, how do I provide the details again for what I want refined? regards Stefan du Plessis CUBIC South Africa

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Incorporating T2 and T1 images in recon-all
by Dan Dillon 03 May '10

03 May '10

Dear FreeSurfers, I have 2 identical structural scans for my subjects: one is T1-weighted and the other is T2-weighted. Is it possible to pass both scans to recon-all? The T1-scans are rapidly acquired MEMPRAGEs, and recon-all seems to be having some difficulty distinguishing cortex from dura around the sagittal sinus. I thought adding the T2-weighted scan into the mix might improve things a bit. Can this be done, and if so, how? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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Re: [Freesurfer] Vertices to matrix coordinates
by f.leone＠donders.ru.nl 03 May '10

03 May '10

Dear Doug, Thanks a lot for the fast reply. I got it to work with your tips. The missing link for me was especially that I could get the vertices locations by using read_surf over the mgz file. Instead of the fmri_info rotation matrix I can also use the matrix from the nii-file, can't I? They are almost exactly equal. Now I got the tal coordinates and try to convert them to indices in my nii matrix. I now do that by add the origin of the nii scan to the found tal coordinates (converted to mni or not). But this makes the brain end up too high in the figure. Any idea how this can be? This is true irrespective of the rotation matrix I take. Thanks a lot in advance, it looks really promising, kind regards, Frank ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Frank Leoné" <f.leone(a)donders.ru.nl> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Monday, May 3, 2010 5:55:33 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Vertices to matrix coordinates The coordinate system is not easy to explain in an email. There are power point slides on our wiki about the geometry used. To get from surface xyz to column, row, slice in the orig.mgz, first get a matrix from the orig.mgz with mri_info --tkrvox2ras orig.mgz this will be 4x4, multiply the inverse of this matrix by the surface xyz (adding a one to make it 4x1) to get the col, row, slice in the orig. doug f.leone(a)donders.ru.nl wrote: > Hi all, > > I checked quite a number of previous posts, but still can't seem to figure out what the vertices numbers given by read_annotation in matlab stand for. My questions are: > > - In what reference frame are they? > - How do I convert them to coordinates in my original structural image (an x * y * z matrix, based on a nii-file)? > > Thanks a lot in advance! > > kind regards, > > Frank > > > -- 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 -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Vertices to matrix coordinates
by f.leone＠donders.ru.nl 03 May '10

03 May '10

Hi all, I checked quite a number of previous posts, but still can't seem to figure out what the vertices numbers given by read_annotation in matlab stand for. My questions are: - In what reference frame are they? - How do I convert them to coordinates in my original structural image (an x * y * z matrix, based on a nii-file)? Thanks a lot in advance! kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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orientation of the data
by Janani Dhinakaran 03 May '10

03 May '10

Hello experts, I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse section and the transverse was in the sagital section. I wonder if there is a place where I can send the data for someone to see and tell me how exaclty to flip the orientation of it to suit FreeSurfer. I would also like to know whether there is a shorter way of processing the data for only mri-stats without running recon-all for all the subjects' data we have. Thank you Jan

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cortical thickness calculation
by miro drahos 30 Apr '10

30 Apr '10

Dear Surferteam, I have been trying to understand details on how the cortical thickness is calculated. I read in the article: "we compute the closest vertex on the pial from each vertex on the white, and vice-versa, then set the thickness to the average of the two." I have tried to carry out this calculation myself, using the generated surfaces lh.white and lh.pial and compare my results to the thickness generated by FS (lh.thickness). There is a one-to-one correspondence between the vertices of the white and pial meshes, which makes it quite straightforward: e.g.: Vertex 100 on white surface has distance from pial surface = 2.5 mm, vertex 100 on pial surface has distance from white surface = 2.6 mm, average == thickness at vertex 100 = 2.55 mm. However, the results that I am getting are different from lh.thickness. I expected discrepancies on the order of rounding errors, but half of the thickness values differ more than 0.001, with some differing as much as 2 mms! What am I missing? Could you please elaborate a bit on how you define the cortical thickness? Thank you very much, Miro Drahos

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Re: [Freesurfer] nu-correct parameters
by Nick Schmansky 30 Apr '10

30 Apr '10

as long as the special parameters for nu_correct are the last ones in the parameter string, after the -all flag. On Fri, 2010-04-30 at 10:45 +0200, Leonardo Chesi wrote: > Hi Nick, > > tank a lot for your help. I’ve tried to launch the segmentation as you > had write me but I received back some errors. So I have try to add to > the command line the –autorecon-all parameters because it try to find > some volumes that there wasn’t in that folder. With the –autorecon-all > parameters the segmentation is started and I’m waiting for the results > that I can see when I come back to work on Monday. I hope that adding > the –autorecon-all parameters is all ok. I wait for your courteous > reply for that parameters. If you need more information about the > error I can send you on Monday the terminal window. > > hoping that my mail has not bothered you, and thank you for the help, > sincerely > > Leonardo > >

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Re: [Freesurfer] nu-correct parameters
by Leonardo Chesi 30 Apr '10

30 Apr '10

Hi Nick, tank a lot for your help. I've tried to launch the segmentation as you had write me but I received back some errors. So I have try to add to the command line the -autorecon-all parameters because it try to find some volumes that there wasn't in that folder. With the -autorecon-all parameters the segmentation is started and I'm waiting for the results that I can see when I come back to work on Monday. I hope that adding the -autorecon-all parameters is all ok. I wait for your courteous reply for that parameters. If you need more information about the error I can send you on Monday the terminal window. hoping that my mail has not bothered you, and thank you for the help, sincerely Leonardo

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FMRI values at surface vertices?
by Dickinson, Annelise (NIH/NIMH) [F] 29 Apr '10

29 Apr '10

Hi all, Sorry if this is a dumb question-is there any way to create a Matlab-readable (e.g. Text) file containing the fMRI values at each surface vertex of a painted surface? Please let me know if you have any idea! Thank you so much, Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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