Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Optseq2 - Incorporate sequential order of trials as a factor
by Gaber, Tilman 26 Feb '10

26 Feb '10

Dear mailinglist recipients, I am currently planning an optimized experiment using optseq2 and a 2x2 factors behavioral response task (Simon-task). The task consists of a pseudo-randomized series of two kinds of trials (congruent and incongruent). In addition there is a sequential factor, i.e. it is of interest whether a trial follows a trial of the same or the opposite kind. In other words there are (2x2) four different conditions where trials relate to precedent trials (AA,AB,BB,BA). Would it be possible to incorporate this sequential factor into the optseq2? I am aware that null events will fall between trials and thus interrupt trial sequences. Trials following null events would therefore be treated separately (i.e. for data analysis). In order to obtain an equal number of trials per condition, this would require increasing the number of trials depending on the number and order of null events. Currently I am able to produce a randomized order of equally balanced trials regarding trial type and sequential order (AA,AB,BB,BA). Any thoughts or suggestions are more than welcome! Best, Tilman

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Gaussian Curvature Calculation
by Lisa Ronan 26 Feb '10

26 Feb '10

Hi All I wonder could you tell me how Gaussian curvature values are computed at a vertex, i.e. Gauss_Bonnet scheme? Is there any way to vary the neighborhood over which the vertex curvature values are computed? Thanks for your help, Lisa Ronan - - - - - - - - - - Research Associate Brain Mapping Unit Sir William Hardy Building Department of Psychiatry University of Cambridge

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how to use time points
by Guang Zeng 26 Feb '10

26 Feb '10

Hi, there, I have scans from two time points, and they have been cross-sectionally processed. But both of they missed some white matter in some slices, so I manually add control points to them, and re-run it. Both of them look fine now. Then, I send them to longitudinal stream. After the -base step is finished. I load the output in the based folder, those white matter are misclassified at the same place again. Is a method which can use the control points I added to the two time point when I called recon-all -base to build the base template. Or I need add control points to the built base subject again? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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can't change common-space subject in qdec
by Danielian, Laura (NIH/NINDS) [E] 25 Feb '10

25 Feb '10

Hi, I've created an average brain and would like to use that as the "common-space subject" in my qdec analysis. However, the program does not seem to allow editing of that box - I can't seem to delete or type over the default fsaverage. Is there a trick to changing this information or another way to load it at the command line? Thanks in advance for your help, Laura

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LGN label or ROI....
by Ritobrato Datta 25 Feb '10

25 Feb '10

Hi All, Is there a method for obtaining an ROI for the lateral geniculate nucleus in freesurfer ? Thanks, Ri

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correction of pial surface...
by Gonzalo Rojas 24 Feb '10

24 Feb '10

Hi: How can I correct the pial surface in the image that I am sending attached ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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QDEC covariate question
by lordowen 24 Feb '10

24 Feb '10

Dear freesurfer experts: We are using freesurfer to preform a cortical thickness analysis between patients and controls. We plan to use the mean_thickness and subject age as covariates. It's fine to analysis as group x age or group x mean_thickness, respectively. But when we set design as group x age x mean_thickness, an error report appeared in the terminal: -------- Matrix condition is 11355.6 ERROR: matrix is ill-conditioned or bad scaled, condno = 11355.6 Possible problem with experimental design: Check for duplicate entries and /or lack of range of continuous variables within a class. (continuous with values in Xg.dat) ------ Does the problem course by the different "range" from age value (between 18-28) and mean_thickness (between 2-4) with in the same subject? if so, how can we solve it? Does proportional scaling on age or mean_thickness help? Any comments are welcome and very appreciate. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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mkanalysis-sess
by Samantha Clark 24 Feb '10

24 Feb '10

Hi, I have a question regarding creating a paradigm file and the command mkanalysis-sess. I am trying to analyze resting state data and wanted to know what the contents of the paradigm file should be. Also what would my mkanalysis-sess command be? Not sure what the -designtype and other options would be in this case. Can you please help? Thanks, Samantha

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nmr-std-env error on seychelles
by Maximilien Chaumon 24 Feb '10

24 Feb '10

Hi Freesurfers, I have an issue with a job I launch on seychelles. I get this error message: /usr/local/freesurfer/nmr-std-env: line 98: syntax error near unexpected token `(' /usr/local/freesurfer/nmr-std-env: line 98: ` set path = ( /usr/pubsw/bin $path )' /var/spool/PBS/mom_priv/jobs/1258634.sey.SC: line 13: isxconcat-sess: command not found Since this is not a file I edited myself, I wonder what's wrong... Thanks, Max

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convert vertex in tksurfer to point in tkmedit
by Guang Zeng 23 Feb '10

23 Feb '10

Hello, there, I load lh.inflated of a subject using tksurfer, click a point (or vetex), then Click "Save Point") Meanwhile, I load the same subject in tkmedit, select "goto save point", I can see the saved point. If I try to convert multiple points (or vertices) from tksurfer to tkmedit, is there an equation? I guess I am looking for the equation which can convert Vertex RAS to Volume Index. Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/

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