Freesurfer December 2008

freesurfer@nmr.mgh.harvard.edu

65 participants
107 discussions

define ROI
by GaBbo Go. Es. 01 Jan '09

01 Jan '09

does anyone know the command line to convert an *.mhg or *.img to a label on freesurfer???'Gabriel. _________________________________________________________________ Comparte hasta 500 fotos en un solo email con Windows Live http://download.live.com/

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QDEC DOSS description bug
by Michael Harms 30 Dec '08

30 Dec '08

Hello, I noticed that when you run a QDEC analysis (QDEC 1.1 in FS 4.1.0) using a "DOSS" model with 1 class (e.g., group) and 1 continuous variable (e.g., age), you still get a putative map for "Does the thickness-age correlation differ between GrpA and GrpB?" (i.e., lh-Diff-GrpA-GrpB-Cor- thickness-age). There should be no such map available for a DOSS model, and a quick check of the contrast vectors indicates that the model is really a duplicate of "Does the correlation between thickness and age, accounting for group, differ from zero?" (i.e., lh-Avg-thickness-age- Cor) cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Transformation from volume index to vertex index
by Yunjie Tong 24 Dec '08

24 Dec '08

Hi freesurfer experts, I have a single subject anatomical data in freesurfer. If I know the volume index of a point on the surface of the cortex ( from T1.mgz in TkMedit), how can I find out the corresponding vertex index or the vertex RAS in TkSurfer. Thanks. BTW, I am using matlab. Thanks, Yunjie

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To FSCourse registrants on/after Dec 18th
by Krish Subramaniam 23 Dec '08

23 Dec '08

Hi all, For those who registered to our Freesurfer course (Jan 20,21 - 2009) *on* or *after* Dec 18th, 2008.. due to a bug in our registration page, we don't have your registration information in our database. We request you to please re-register using that page again http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.cgi Sorry for the trouble. Krish

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(no subject)
by Gabriel GLZ 23 Dec '08

23 Dec '08

first - wich is the command line for transform an *.img o *.mgh to *.label second. I have a program that gave a PET mask (*.img) with a specific region of activation, I want to know wich are the vertex of that region, to take them to FS and to create a label for making the thickness of that specific zone of mayor metabolic consume another program gave a *.mgh that contains specific areas of significance of cortical thickness between groups. those areas are different of the parcellation generated by FS, i want to take that *.mgh to create a specific label on FS that only contains that areas of significance and make the measurements with FS thnx. Gabriel. _________________________________________________________________ Arrastrar y colocar: acceso muy fácil al uso compartido de fotos con Fotos de Windows Live™. http://www.microsoft.com/windows/windowslive/photos.aspx

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Re: [Freesurfer] group analysis
by Bruce Fischl 22 Dec '08

22 Dec '08

Hi Feng-Xian, 1,2. Not sure what you mean. We certainly compute the p from a t or an F and save all of the above. 3. Yes, we can display either individual subject maps of thickness (?h.thickness) or effects sizes after GLM analysis, or group means if you want. cheers Bruce On Mon, 22 Dec 2008, b9403208 wrote: > > To Dear: > I would make sure of the results of the group analysis. > 1. The p-value, actually -10log(p), is only used in the qdec display. > That is to say, the value is used to display the difference of the two > groups. > 2. And Freesurfer doesnt use any statistical significance values, like, > statistical p-value, T-value, z-score at present. > 3. Freesurfer cant display the cortical thickness in unit, mm. So, I get > the conclusion that Freesurfer couldnt quantify the cortical thickness > at present. > > Thank you in advance. > > Feng-Xian > > > ------------------------------------------------- > Chang Gung University Mail Server Web Mail system > By Chang-Gung University Information Center > (http://www.cgu.edu.tw/ic/) > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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surface cluster area bug
by Doug Greve 22 Dec '08

22 Dec '08

Hi Y'all, I've recently found an error in the way that mri_surfcluster reports the area of a cluster when using a group surface such as fsaverage. The bottom line is that the area reported is about 25% too big. However, the cluster-wise p-values reported by mri_surfcluster based on simulations from mri_glmfit ARE NOT AFFECTED. Volume clustering is unaffected. I have fixed this bug in the Martinos Center "dev" environment. Part of this fix is to make old versions of mri_glmfit simulation incompatible with new versions of mri_surfcluster (and vice versa) for surfaces (ie, mri_surfcluster will exit with an error or will crash -- either way, it will not complete), as this could generate erroneous p-values. We will be propagating the fix to our stable version after the holidays, and make new distributions available. More info and updates can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface As always, sorry for the bug. doug ps. On the brighter side, I discovered this bug while implementing gaussian random field (GRF) corrections for multiple comparisons, so soon you will be able to run GRF in seconds instead of running monte carlo simulations over a weekend. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Thanks for the answers
by Yunjie Tong 22 Dec '08

22 Dec '08

Hi Doug and Bruce, Thanks for your answers. One more question, why the vertex RAS of the same spot on the brain given in TkSurfer is not the ones I read by Matlab program freesurfer_read_surf? The commands I am using are: [vertex_coords, faces] = freesurfer_read_surf('tutorial_subjs/subject/ surf/lh.inflated'); tksurfer subject lh inflated Thanks, YJ if you have the voxel index (col, row, slice) then you can: V2R = [ -1.00000 0.00000 0.00000 128.00000 0.00000 0.00000 1.00000 -128.00000 0.00000 -1.00000 0.00000 128.00000 0.00000 0.00000 0.00000 1.00000 ] crs = [col row slice]'; xyz = V2R[crs+1; 1]; then find the vertex whose xyz coors are closest to xyz Yunjie Tong wrote: > Hi freesurfer experts, > > I have a single subject anatomical data in freesurfer. If I know > the volume index of a point on the surface of the cortex ( from > T1.mgz in TkMedit), how can I find out the corresponding vertex > index or the vertex RAS in TkSurfer. Thanks. BTW, I am using matlab. > > Thanks, > > Yunjie > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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group analysis
by b9403208 22 Dec '08

22 Dec '08

To Dear: I would make sure of the results of the group analysis. 1. The p-value, actually -10log(p), is only used in the qdec display. That is to say, the value is used to display the difference of the two groups. 2. And Freesurfer doesn’t use any statistical significance values, like, statistical p-value, T-value, z-score … at present. 3. Freesurfer can’t display the cortical thickness in unit, mm. So, I get the conclusion that Freesurfer couldn’t quantify the cortical thickness at present. Thank you in advance. Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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some questions
by Siddharth Srivastava 20 Dec '08

20 Dec '08

Hi everyone, what is the difference in functionality between the mri_* commands and the mris_* commands? How does the mris_fill command maintain the distinction between the left and the right hemisphere? I see only one filled.mgz having 2 labels? does it write to the same file during each invocation (lh,rh), or just one call is enough to fill both hemispheres? mris_morphology: it is possible to specify the structuring element for the intended operation? best regards, sid

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Freesurfer December 2008