Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

freesurfer and DTI
by Dana W. Moore 12 Mar '10

12 Mar '10

Hello everyone, I have a colleague (cc'd) who is interested in using FreeSurfer's segmentation with DTI results he obtained with TBSS. I am not sure how he should go about this. Any advice is appreciated. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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optseq installation
by Florence POMARES 12 Mar '10

12 Mar '10

Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2

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problem on recon-all
by Xiaoying Tang 12 Mar '10

12 Mar '10

Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated in autorecon2 and autorecon3. Is there any way to do this? Looking forward to your early reply. Best, Xiaoying

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Performance on brains with tumors
by Chris Filo Gorgolewski 12 Mar '10

12 Mar '10

Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris

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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

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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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