Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

Bad pial surface
by Ed Gronenschild 12 Mar '10

12 Mar '10

Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Intel. Ed

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bbregister
by corinna bauer 11 Mar '10

11 Mar '10

Hello, I am running bbregister with pet scans and a number of the subject's registrations were poor. What is the best way to fix inaccurate coregistrations from bbregister? Regards, Corinna

3 3

within subject regression analysis and qdec
by Katie Bettencourt 11 Mar '10

11 Mar '10

Hi, I'm still trying to figure out how to run a regression analysis using functional data. I found the information in using qdec, however, the example uses a between subject design (with age/gender) and looks at thickness measures. I tried creating a qdec.table.dat, but I am unsure how to do it with a within subject design, as when I ended up with it reading the file as me having 16 subjects instead of 8. What I have is a discrete variable of load (high and low) and a continuous variable of set size (1,3,6), but I want to correlate the data with the performance at each set size for each load as well as load. This is what my qdec table looked like: fsid dist k1 k3 k6 subj1 low 1 2.9 4.0 subj1 high 0.8 1.3 2.0 subj2 low 0.9 2.9 5.7 subj2 high 0.9 1.9 1.4 ... subj8 low 0.8 2.4 2.5 subj8 high 0.8 1.4 2.7 Can anyone tell me how to appropriately structure this to do what I want? Thank you! Katie

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Qdec Analysis Interpretation
by johanna feiler 11 Mar '10

11 Mar '10

Dear Freesurfers, in my qdec analysis I want to compare my patients group with a control group. The analysis should be corrected for age effects, so I used group as discrete factor and age as covariate. If I choose „Does the average thickness differ between the two groups“, how can I interpretate a significant result in a certain region? Does it mean: „The mean thickness in this region differs between both groups significantly, correcting for age effects“? I got some highly significant results, however the groups' means don't seem to differ that much, however, the groups' trends seem to be quite different. So which statistical test is implemented ins qdec? Any help will be appreciated! Thanks a lot, Johanna Feiler ___________________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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brainmask/wm edits
by Helen Keefe 11 Mar '10

11 Mar '10

Hi, I have a similar questionto the one listed below. After I edit brainmask.mgz and wm.mgz, my understanding was that I could run autorecon2-wm and would not have to run autorecon2-pial because -wm will run everything else through the end of -autorecon2. However, if brainmask.mgz is run at the end of autorecon1, don't I need to run autorecon1 again, since wm or contol point edits would alter the brainmask?? Thanks for help, Helen ____________________________________________________________ "Hi Dana, you can do autorecon2-cp and it will do both things (the wm comes after it in the stream anyway) cheers Bruce On Tue, 9 Mar 2010, Dana W. Moore wrote: > Hello everyone, > > There is an image that needs white matter edits (editing voxels) as > well as control points. I know the two commands I need to re-run are > autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and > somehow combine the -cp and -wm commands, or do I need to do the > control points first, re-run, and then do further white matter edits? > > Thanks, > Dana > -- Helen L. Keefe Mental Health Clinical Research Center Image Processing Lab University of Iowa 319-353-8586

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w file conversion
by Yigal Agam 11 Mar '10

11 Mar '10

Hi, Is it possible to convert a .w file to another format? Thanks, Yigal

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Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
by jijun wang 11 Mar '10

11 Mar '10

Dear FS experts, I am using CentOS 5.4. When I run tkmedit, the data looks fine. In tksurfer, it just appears as a sliver of surface without an error message. In console, it sticks on reading vertex. Somebody said this could be resolved by simply removing the package xserver-xgl. How can I do this? Any advice would be highly appreciated. -- Best regards, Jijun Wang, MD & PhD Shanghai Mental Health Center 600 Wanping Road Shanghai 20030, China. E-mail: jijunwang27(a)gmail.com

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a question about FS longitudinal stream
by Guang Zeng 10 Mar '10

10 Mar '10

Hi, there, I have a question about FS longitudinal stream, I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine. When I ran the longitudinal stream, one of them stopped at the first step, it failed to do the skull stripping. I changed the watershed threshold, it works now. The question is, for this time point data, I want to use the following command line to finish the rest longitudinal analysis, recon-all -long tp_dat1 base_id -autorecon2 -autorecon3 Is it correct? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Longitudinal Stream...
by Gonzalo Rojas Costa 10 Mar '10

10 Mar '10

Hi: I processed a Longitudinal Stream between two MRIs of same patient taken in different dates... I used the following commands: i) recon-all -all -s <tp1id>, recon-all -all -s <tp2id> ii) recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all iii) recon-all -long <tp1id> <templateid> -all Which information was stored in the <tp1id>.long.<templateid> folder ?... Sincerely, Gonzalo Rojas Costa

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freesurfer atlas and template
by Guang Zeng 10 Mar '10

10 Mar '10

Hello, there, I have two questions about FreeSurfer default atlas and template, Will Freesurfer team build an atlas or template using 3T scans in future? Will Freesurfer team build an atlas or template using patients with disease in future? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/

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Freesurfer March 2010