Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

drawing adjacent labels with shared boundaries, and labels near the edge of a patch
by Lindsay Lewis 18 Mar '10

18 Mar '10

hi, I am trying to manually draw a "grid" of many small ROIs/labels on an occipital flattened surface patch in tksurfer, and am having 2 points of confusion: (1) I want my labels to be directly adjacent to each other, but since I am drawing manually, I am not sure how to use the boundary of one label to define the boundary of the adjacent label? (obviously, recreating the shared boundary manually each time will likely not be exactly identical - there could be some voxels accidentally left out between the two labels, or some voxels accidentally common to the two labels) (2) I have some labels I want to extend all the way to the edge of the patch. I keep doing my best to mark the vertex at the very edge, but I keep ending up marking a vertex not all the way at the edge, or slightly out in empty space beyond the patch. I am not sure how to mark the very edge of the patch. If anyone has any advice regarding how to address these two issues, I would very grateful! Many thanks.

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Replicating qdec analysis with more than 2 continuous variables
by Laluz, Victor 18 Mar '10

18 Mar '10

Hello Freesurfer folks, I hope this question is simple to answer: Is there any way to do a surface-based group analysis, a-la qdec, without the limitation of 2 continuous variables? My goal is to analyze a thickness relationship with continuous variable X, which I have so far analyzed controlling for variable Y. However, I ALSO want to control for variable Z. As it is in qdec, it forces me to select only 2 of either X Y and Z. I have tried converting one of the variables to a discrete factor, but the results do not look the same at all. Any advice you can give will be very appreciated; and, as we are currently working under a deadline of sorts, the sooner someone might get back to me the better... as always, I really appreciate the help. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax)

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tksurfer and tcl scripting: looping over subjects
by Carrie Niziolek 18 Mar '10

18 Mar '10

Hello all, I've had great success using tcl scripts to loop over surfaces and overlays for a given subject. Are there scripting options for looping over subjects? The problem I see is that the call to tksurfer initializes the subject ("tksurfer subjid lh inflated -tcl myscript.tcl"), and I'm unsure how to change the subjid inside the tcl script. How can I invoke tksurfer inside a tcl script? I found another post asking the same question, but I couldn't find a response: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02344.html One workaround would be to do the loop from the shell, invoking a separate instance of tksurfer for each subject/hemisphere, but in that case I'm unsure how to quit tksurfer from the shell after each call (instead of winding up with dozens of tksurfers running simultaneously). Any advice would be appreciated. Many thanks, Carrie

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research jobs in San Francisco, CA
by Brian Roach 18 Mar '10

18 Mar '10

Dear Freesurfer users, We are hiring for multiple positions in our San Francisco-based schizophrenia brain-imaging EEG research lab. Please visit the links below for additional details: <http://jobs-ncire.icims.com/jobs/1504/job>http://jobs-ncire.icims.com/jobs/1504/job http://jobs-ncire.icims.com/jobs/1505/job Thank you, Brian

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Averaging cortical thickness maps
by Xiaojing Long 18 Mar '10

18 Mar '10

Hi, I have a question regarding how to average cortical thickness maps. I have a dataset with 10 MR brain images and I've run recon-all on each of them. So I've got thickness maps ?h.thickness for each subject. I wonder whether freesurfer provides a tool that can average the cortical thickness maps over the dataset. Thanks. Best, Xiaojing

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showing all slices in freeview
by ythomas 18 Mar '10

18 Mar '10

Hi, is it possible to show all slices (or every N slices) of a volume in freeview in a particular orientation (e.g. axial or coronal)? Thanks, Thomas

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Model setup - comparing correlations
by Martin Kavec 18 Mar '10

18 Mar '10

Hi, in my group analysis I found a significant difference in correlation of physiological parameter X and cortical thickness Y1 in an ROI. For each subject and each cortical parcel I also have a average of parameter Y2 and its correlation to X (calculated using GLM in SPSS). Y1 ~ X Y2 ~ X My question is, whether there is any meaningful approach how to test whether for any cortical parcel correlation between Y1 ~ X and Y2 ~ X are statistically different/similar? This kind of resembles me a conjunction analysis in fMRI, but I am not sure how would I test this. Also - and sorry for slight off topic - I think that SPSS should be my friend. Many thanks for suggestions, Martin

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Talairach_MNI
by Kelly Silva 18 Mar '10

18 Mar '10

Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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q about disc space
by Janani Dhinakaran 17 Mar '10

17 Mar '10

Hello. How much space is required for running one recon-all? If I needed to work on several people's brains, say 4-5, how much memory am I likely to need? Thanks! -- I am the Sun, I know no darkness.

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segmentation using freesurfer
by Xiaoying Tang 17 Mar '10

17 Mar '10

Hi All, Is it possible to get only csf via using freesurfer to do segmentation? Best, Xiaoying

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Freesurfer March 2010