## marsbar-users

 Re: [Marsbar-users] [SPM] center of mass From: Matthew Brett - 2012-11-24 19:41:06 Hi, I've forwarded to the marsbar mailing list... On Sat, Nov 24, 2012 at 3:23 AM, SUBSCRIBE SPM Veda wrote: > Dear SPM experts, > > When I used the marsbar to extract the beta value, I got two identical beta values across in two different coordinates (-44, -64, -16 and -28, -94, -8). It is strange because they had different p values and I supposed that they should have had different betas. When I view the two ROIs in the marsbar, I found that they had identical center of mass. Does it mean they belong to the same cluster? BTW, the spatial resolution is 3.4mm x 3.4mm x 3.4mm and smooth at 8mm x 8mm x 8mm. Can any one tell me why the different coordinates had the same beta? > The p value comes from dividing the contrast value by its variance. If your contrast just selected the single beta value, the variance can still differ, and therefore the p value. Are the beta values identical to all decimal places? How about the con_**.img values in the same location (the top half of the t contrast)? How did you extract the beta values for these two coordinates exactly? Best, Matthew
 Re: [Marsbar-users] [SPM] center of mass From: Matthew Brett - 2012-11-25 02:21:00 Hi, On Sat, Nov 24, 2012 at 3:40 PM, a489930026 wrote: > Hello Dr. Brett, > > Thank you for your quick response! > To extract the beta, I clicked on the coordinates on the statistic table and > used "get SPM cluster" in Marsbar to save the ROIs. Then, I used the > following codes to obtain the beta from every subject: > > VY = spm_vol( P ); > rois = {'wrd-bl_-28_-94_-8_roi','wrd-bl_-44_-64_-16_roi'} > for i = 1:length(rois) > roi = maroi('load',strcat(rois{i}, '.mat')) > mm = get_marsy(roi, VY, 'mean'); > > And to your question, the betas were identical to all decimal places and the > con_**.img values were different. Just to check: VY = spm_vol( P ); rois = {'wrd-bl_-28_-94_-8_roi','wrd-bl_-44_-64_-16_roi'} nrois = length(rois); mm = cell(1, nrois); for i = 1:length(rois) roi = maroi('load',strcat(rois{i}, '.mat')) mm{i} = get_marsy(roi, VY, 'mean'); Do you get identical data ? I mean, what is the result of: >> summary_data(mm{1}) - summary_data(mm{2}}) ? Best, Matthew
 Re: [Marsbar-users] [SPM] center of mass From: Veda - 2012-11-26 15:20:02 Matthew Brett gmail.com> writes: > > Hi, > > On Sat, Nov 24, 2012 at 3:40 PM, a489930026 yahoo.com.tw> wrote: > > Hello Dr. Brett, > > > > Thank you for your quick response! > > To extract the beta, I clicked on the coordinates on the statistic table and > > used "get SPM cluster" in Marsbar to save the ROIs. Then, I used the > > following codes to obtain the beta from every subject: > > > > VY = spm_vol( P ); > > rois = {'wrd-bl_-28_-94_-8_roi','wrd-bl_-44_-64_-16_roi'} > > for i = 1:length(rois) > > roi = maroi('load',strcat(rois{i}, '.mat')) > > mm = get_marsy(roi, VY, 'mean'); > > > > And to your question, the betas were identical to all decimal places and the > > con_**.img values were different. > > Just to check: > > VY = spm_vol( P ); > rois = {'wrd-bl_-28_-94_-8_roi','wrd-bl_-44_-64_-16_roi'} > nrois = length(rois); > mm = cell(1, nrois); > for i = 1:length(rois) > roi = maroi('load',strcat(rois{i}, '.mat')) > mm{i} = get_marsy(roi, VY, 'mean'); > > Do you get identical data ? I mean, what is the result of: > > >> summary_data(mm{1}) - summary_data(mm{2}}) the script got stocked with the following errors. Undefined function or method 'summary_data' for input arguments of type 'cell'. and when I ran "summary_data(mm{1}) - summary_data(mm{2}})". it returned: Error: Unbalanced or unexpected parenthesis or bracket. Veda >
 [Marsbar-users] Running Marsbar as MATLAB Script or from Command Prompt From: Kwaku Akrofi - 2012-11-26 23:44:38 Attachments: Message as HTML Hi MarsBar-ers,   My question today is about how to run MarsBar through a MATLAB script or a MATLAB command prompts to avoid the need to run it interactively through the GUI. What are the commands I need to know to allow command prompt operation?   To be more specific, I am currently creating a spherical ROI, finding the mean value of the ROI across time (scans), and storing this timecourse as a text file. This is how I am approaching it via the GUI:   1. ROI Definition -> Sphere [I enter the coordinates of the center of the sphere and proceed from there.] 2. Design -> Set design from file. [Here, I choose the SPM.mat file for a prior GLM analysis on an individual.] 3. Data -> Extract ROI (default).  [I select the ROI created in Step 1.] 4. Results -> Estimate Results 5. Data -> Export Data -> Summary time course(s) for region(s) -> Text file.   I have to repeat these steps for numerous ROIs in numerous subjects, so I would like to know how to bypass the GUI and do it via an m-file. I am running SPM8 in MATLAB R2010b, and I use MarsBar 0.43.   Thank you very much in advance for the help.   Kwaku.
 Re: [Marsbar-users] Running Marsbar as MATLAB Script or from Command Prompt From: James Lee - 2012-11-27 16:30:31 Kwaku, A good first step is the batch script in marsbar/examples/batch/run_tutorial.m . Many of the steps you are interested in are illustrated there. Hope this helps! Jim Lee On 11/26/12, Kwaku Akrofi wrote: > Hi MarsBar-ers, > > My question today is about how to run MarsBar through a MATLAB script or a > MATLAB command prompts to avoid the need to run it interactively through the > GUI. What are the commands I need to know to allow command prompt operation? > > To be more specific, I am currently creating a spherical ROI, finding the > mean value of the ROI across time (scans), and storing this timecourse as a > text file. This is how I am approaching it via the GUI: > > 1. ROI Definition -> Sphere [I enter the coordinates of the center of the > sphere and proceed from there.] > 2. Design -> Set design from file. [Here, I choose the SPM.mat file for a > prior GLM analysis on an individual.] > 3. Data -> Extract ROI (default). [I select the ROI created in Step 1.] > 4. Results -> Estimate Results > 5. Data -> Export Data -> Summary time course(s) for region(s) -> Text file. > > I have to repeat these steps for numerous ROIs in numerous subjects, so I > would like to know how to bypass the GUI and do it via an m-file. > I am running SPM8 in MATLAB R2010b, and I use MarsBar 0.43. > > Thank you very much in advance for the help. > > Kwaku.
 Re: [Marsbar-users] Running Marsbar as MATLAB Script or from Command Prompt From: Carsten Zuehlsdorf - 2012-11-28 11:17:27 Hello, I have written a matlab script to do the following: 1. ROI Definition - Select SPM Cluster 2. Design - Set design from file 3. Data - Extract ROI (default) 4. Results - Estimate Results 5. Get % Signal Change and Statistical Table I could send you that one if it's any help. I made it mostly by combing through the source code of MarsBaR and SPM. ----- Ursprüngliche Mail ----- Von: "Kwaku Akrofi" An: "MarsBaR users list" Gesendet: Dienstag, 27. November 2012 00:44:31 Betreff: [Marsbar-users] Running Marsbar as MATLAB Script or from Command Prompt Hi MarsBar-ers, My question today is about how to run MarsBar through a MATLAB script or a MATLAB command prompts to avoid the need to run it interactively through the GUI. What are the commands I need to know to allow command prompt operation? To be more specific, I am currently creating a spherical ROI, finding the mean value of the ROI across time (scans), and storing this timecourse as a text file. This is how I am approaching it via the GUI: 1. ROI Definition -> Sphere [I enter the coordinates of the center of the sphere and proceed from there.] 2. Design -> Set design from file. [Here, I choose the SPM.mat file for a prior GLM analysis on an individual.] 3. Data -> Extract ROI (default). [I select the ROI created in Step 1.] 4. Results -> Estimate Results 5. Data -> Export Data -> Summary time course(s) for region(s) -> Text file. I have to repeat these steps for numerous ROIs in numerous subjects, so I would like to know how to bypass the GUI and do it via an m-file. I am running SPM8 in MATLAB R2010b, and I use MarsBar 0.43. Thank you very much in advance for the help. Kwaku. ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from \$795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ Marsbar-users mailing list Marsbar-users@... https://lists.sourceforge.net/lists/listinfo/marsbar-users