http://blog.gmane.org/gmane.comp.graphics.spm.marsbar hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1505 <pre>To whom it may concern: I am trying to do the roi batch analysis on my fmri data. But I encounter a problem. For some subjects data, I could not open the image file. See the error message below: MarsBaR analysis functions prepended to path Design reporting : ...done Fetching data : 1/1 ??? Error using ==&gt; spm_sample_vol Cant open image file. Error in ==&gt; maroi.getdata at 103 data = spm_sample_vol(data_imgs(i),... Error in ==&gt; maroi.get_marsy at 76 [y vals vXYZ mat] = getdata(o, VY); Error in ==&gt; marsbar at 985 marsY = get_marsy(o{:}, VY, sumfunc, 'v'); Error in ==&gt; spm at 982 evalin('base',CBs{v-1}) ??? Error while evaluating uicontrol Callback I ever tried to search on the mailinglist to find some answers. But it seems that there are no definitive replies. Does anyone here know about it and how to fix it? Thanks for your consideration in advance. Best, li ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ </pre> Yansong 2012-05-25T10:04:26 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1500 <pre>Hi, When I did SPM analysis, I modeled the events with HRF and both time derivative and dispersion derivative. Will this affect the percent signal change calculation? And we also have a default baseline (directional arrow images), will this affect the reliability of the method? Can area under the curve calculation be an alternative method for ROI analysis? Thank you! Yan ________________________________ UT Southwestern Medical Center The future of medicine, today. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Yan Fang 2012-04-27T23:09:56 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1494 <pre>Hey All, A couple of questions regarding some of the options/functions of Extract Roi(Full Options)... 1. Is it appropriate to use this function directly on the .con files generated after running your GLM (assuming that you choose not to specify a SPM.mat)? 2. What is the nature of the value generated when you select raw data? That is, what does the value represent with respect to the contrast I have selected. A colleague of mine suggested that it was derived from the Betas in the selected .con, but I am not so sure. Anyone have any ideas? Thanks in advance, Andrew Furman Graduate Student - Johns Hopkins University ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ </pre> Andrew Furman 2012-04-24T14:47:22 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1493 <pre> Hi all, My fMRI running is just alternating “on” (10 sec) and “off” (20 sec) paradigm. Each subject thus has a first-level t contrast. In another 2nd-level analysis, these 20 t contrasts were also used to correlate with a behavior score. Now I want to know the % signal change (%SC) in a specific ROI in all my 20 subjects. METHOD 1 In the beginning, I extract %SC in this ROI by MarsBar individually: (1)(matlab directory is in the t contrast of subject 1) “design” – “set design from file” – select the contrast image of subject 1 (2)“data” – “extract ROI data (default” – select this ROI (3)“Result” – “estimates results” (4)“Results” – “% signal change” – event 1 = 10, event 2 = 20. Then I got the %SC (value in event 1 – value in event 2) Am I right? By this method, I can finally get 20 numbers (values) representing %SC in this ROI for my group. But that means, I have to repeat these steps 20 times…..time-wasting….. METHOD 2 Then I explored the second method: (1)(matlab directory is in the 2nd-level analysis file now!) “design” – “set design from file” – select the contrast image of 2nd-level SPM file. (2)Same as (2) above. (3)Same as (3) above. (4)“Data” – “Export data” – “Export summary timecourse for region” – “Export to text file” Happily, I opened this text file and I found 20 numbers. However……they were different from those obtained from method 1. But intriguingly, I found the values from both methods were HIGHLY CORRELATED (simple linear regression p&lt;0.0001, r = 1, perfectly fitted to a line which passes through the origin 0,0)! So, which method represents real %SC (or is better) and which method should I use? What’s the relationship between values obtained from both methods? If method 2 is now allowed, any TIME-SAVING way to get the value (instead of method 1)? Thanks a lot! Carlos </pre> CarlosTseng 2012-04-24T01:58:24 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1489 <pre>I have a list of coordinates in MNI space (loads of them) that are listed in a long text file (x y z format) which I would like to define as an ROI in order to sample data with MarsBar. So for example 1000 points listed in a file should be created as one ROI. What would be the most straight forward way to do this? Thanks, Sharon </pre> Sharon Gilaie-Dotan 2012-04-19T05:16:28 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1488 <pre> http://techproindia.in/wp-content/themes/thematic/rofmd.html?ase=wc.php&amp;jkp=fe.php&amp;fry=koqb ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Mac Shine 2012-04-08T14:06:17 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1481 <pre>Dear all, Marsbar is able to extract beta values (parameter estimates) for individual columns in an SPM design matrix. Is it also possible for Marsbar to calculate/extract the variance of these beta values as well? I.e. a variance estimate for each column of the SPM design matrix rather than the whole model variance? Any help would be much appreciated! Thank you! Sara ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> De Simoni, Sara 2012-03-19T17:31:01 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1479 <pre>I am trying to run the following script but I am unable to get the mardo command to recognize the path. D ends up blank even though the variable is created: ****SCRIPT**** subjects = {'10' '20'}; ROIs={'Conj_Gilbert_RaPFC_roi_ST3_28_54_16_roi.mat' 'Gilbert_Lapfc_Conj_PMHit-Ong_ST3_-30_52_12_roi.nii'}; % 'sphere_8--50_-58_22_roi.mat' %ROItypes = {'cluster'; 'sphere'}; %for ROItype = 1:length(ROItypes); for ROI = 1:length(ROIs) for i = 1:length(subjects) %% Load design and ROI %This line is the path to the dubject specific SPM.mat file spm_name = {['/data/path/' subjects{i} '/Functionals/Analyze3/All_effects_mvmt_128/SPM.mat']}; roi_file = {['/data/path/VOIs/' ROIs{ROI}]}; D = mardo(spm_name); R = maroi(roi_file); Y = get_marsy(R, D, 'mean'); xCon = get_contrasts(D); E = estimate(D,Y); E = set_contrasts(E, xCon); b = betas(E); marsS = compute_contrasts(E, 1:length(xCon)); %% Extract and save timecourses [e_specs, e_names] = event_specs(E); n_events = size(e_specs, 2); bin_size = tr(E); fir_length = 25; bin_no = fir_length / bin_size; opts = struct('single', 1, 'percent', 1); for e_s = 1:n_events fir_tc(:, e_s) = event_fitted_fir(E, e_specs(:,e_s), bin_size, bin_no, opts); end %save timecourse %enter path &amp; name of output outputdoc = open(['/data/path/timecourse_' subjects{i} '_' ROIs{ROI} '.txt']); fprintf(outputdoc, '%s\t\n\r',ROI); condition = size(fir_tc); condition = condition(2); for contrastnumber = 1:condition fprintf(outputdoc, '%8.7f\t',fir_tc(:,contrastnumber)); fprintf(outputdoc, '\n\r'); end fclose(outputdoc); end end *****ERROR:***** ??? Undefined function or method 'get_marsy' for input arguments of type 'mardo'. Error in ==&gt; extract_timecourse_PM2 at 31 Y = get_marsy(R, D, 'mean'); ****Variable D***** val = [mardo design object] SPM working dir Design type: Unknown Modality: unknown Has filter?: N/A Has images?: unknown MarsBaR estimated?: no Description: Not specified ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Pamela LaMontagne 2012-03-19T17:06:18 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1478 <pre>Dear Marsbar, I am new to fMRI analysis with SPM and marsbar, but I appreciate marsbar's ease of use and the clarity of the manual. I do have a few simple questions just to make sure I am interpreting my results right. I am at an institution that does not use SPM or marsbar and I am learning on my own so I apologize if these questions are naive. I ran a 2-sample t-test in SPM to investigate differences in activation between patients and controls during painful stimuli vs implicit rest. I then ran an roi analysis in marsbar following the routine used in the tutorial. When you do this procedure is it the case that marsbar is running the 2-sample t-test again only in the rois? For the basic statistics table, is it appropriate to make an inference about regions being significantly different between groups that have a p-value &lt;.05 (this just seemed to simple)? I plotted my "effect of interest" and extracted beta values by typing "y" in the matlab prompt...is it better to run an 2-sample t-test in another stats program with these values or is this redundant? My other question has to do with the % signal change. I have four sessions in my first level design with 40 second stimulation and 40 second rest blocks. When marsbar asks for duration, what does that mean? Would it be the TR or 40 second blocks? Thanks so much in advance, Jessica ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Jessica Wojtalik 2012-03-13T15:30:01 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1477 <pre>Hi everyone, I'm trying to calculate the percentage of voxels in an ROI active above a certain t threshold and I come up against the following error when I run getdata: y = getdata(roi_obj, t_imgs) ??? Error using ==&gt; spm_vol&gt;subfunc at 111 File "spmT_002.img" does not exist. Error in ==&gt; spm_vol&gt;subfunc1 at 84 v = subfunc(P(i,:)); Error in ==&gt; spm_vol&gt;subfunc2 at 70 V = subfunc1(P); Error in ==&gt; spm_vol at 54 V = subfunc2(P); Error in ==&gt; maroi.getdata at 41 data_imgs = spm_vol(data_imgs); Anyone have any ideas how I can fix the problem? Thanks in advance Mac ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Mac Shine 2012-03-13T04:37:43 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1476 <pre>Dear experts, I am trying to use the AAL ROIs from MarsBar in my fMRI analyses. I have normalized all my fMRI to the MNI template using DARTEL, with voxel size set at 3x3x3mm and dimensions 61x73x61. The AAL ROIs however have voxel size 2mm3 and dimensions 91x109x91. Sorry for a very basic question, but what would be the best way to match/register the ROIs to my data? E.g. which normalization procedure and which templates? In addition, what is the difference between using MarsBar's extract ROI data and using the ROI as an explicit mask in standard SPM analysis? Many thanks for your help! Merina Su PhD candidate Institute of Child Health University College London ------------------------------------------------------------------------------ Virtualization &amp; Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Su, Merina 2012-03-07T14:48:23 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1475 <pre>From: Matthew Brett &lt;matthew.brett&lt; at &gt;gmail.com&gt; To: MarsBaR users list &lt;marsbar-users&lt; at &gt;lists.sourceforge.net&gt; Cc: Date: Fri, 10 Feb 2012 10:29:53 -0800 Subject: Re: [Marsbar-users] raw vs. standardized % BOLD signal change Hi, On Fri, Feb 10, 2012 at 6:20 AM, Chaleece Sandberg &lt;challysand&lt; at &gt;gmail.com&gt; wrote: Could you point us to the article? I'm not sure what standardized means in this context. Best, Matthew Hello again, Here is the article that I was reading. The description of using raw versus standardized effect sizes is on page 190. Syntactic processing in the human brain: What we know, what we don’t know, and a suggestion for how to proceed Evelina Fedorenko, Alfonso Nieto-Castañón, Nancy Kanwisher Brain &amp; Language 120 (2012) 187–207 Thanks! Chaleece ************************************************ Chaleece Sandberg, M.A. Ph.D. Candidate Speech Language and Hearing Sciences Boston University Sargent College Lab Manager Aphasia Research Laboratory Email: cws&lt; at &gt;bu.edu Phone: 617-353-2706 ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d </pre> Chaleece Sandberg 2012-03-06T13:13:10 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1472 <pre>Hi, How are you? I'm a new user of MarsBaR. I've written a script following the commands in FAQ to run MarsBaR analysis in batch mode. But mardo.m seemed to not work under SPM5. Is there any solution for this problem? Thank you! Yan ________________________________ UT Southwestern Medical Center The future of medicine, today. ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Yan Fang 2012-03-05T23:51:34 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1471 <pre>Dear All, I am new to MarsBar and SPM8. I want to extract time course, and the example dataset works fine. When I try to use our actual .nii format data to do 'run_preprocess' instead of example data, I get the following error message: MarsBaR analysis functions prepended to path ??? Attempted to access condons(:,2); index out of bounds because size(condons)=[0,0]. Error in ==&gt; er_model_spm2 at 88 tmp = condons(:,2); % get stimulus column Error in ==&gt; configure_er_model at 74 er_model_spm2(sess_dir, sesses, ana_dir); Error in ==&gt; run_preprocess at 26 model_file = configure_er_model(subjroot, sesses{ss}, sdirname); I read some previous posts and tried to change directories but the problem is still unsolved. The spm8_ana folder under sess1 is created during the process but there is no spm.mat file in it. Can anyone give some suggestions? Any help is much appreciated! Cheers, Bo Luan ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 </pre> Bo Luan 2012-03-05T22:47:47 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1470 <pre>Hi All, I am trying to extract raw timecourses from images, and I followed these instructions: "This can be done from the GUI. Select Data - Extract ROI data (full options). Select the ROIs, say No to use SPM design, Other for type of images, 1 for number of subjects. Select the images you want to extract data from, Raw data for scaling, and 0 for grand mean. Now you can plot the data from the GUI, or save in various formats using Data - Export data." However, instead of obtaining a time series, I get a single point. Any guesses what I am doing wrong? Cheers, ES ------------------------------------------------------------------------------ Virtualization &amp; Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/_______________________________________________ Marsbar-users mailing list Marsbar-users&lt; at &gt;lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/marsbar-users </pre> Sejdic, Ervin 2012-03-03T23:18:10 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1468 <pre>Hello, I am reading an article that suggests using raw (unstandardized) effect sizes (% BOLD signal change) rather than standardized effect sizes. Does MarsBaR have this option? If so, how do I find it? Thanks, Chaleece ************************************************ Chaleece Sandberg, M.A. Ph.D. Candidate Speech Language and Hearing Sciences Boston University Sargent College Lab Manager Aphasia Research Laboratory Email: cws&lt; at &gt;bu.edu Phone: 617-353-2706 ------------------------------------------------------------------------------ Virtualization &amp; Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ </pre> Chaleece Sandberg 2012-02-10T14:20:57 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1460 <pre>Hi All, I am trying to figure out command line for extracting ROI data from 90 ROIs (full options), using an SPM design with 72 time-points (3 runs x 24 images/run). When I complete this process in the GUI, these are the steps I follow: 1. 'Extract ROI data' (full options) &gt; Select ROIs 2. Use SPM design &gt; Yes 3. Images from &gt; SPM design 4. Scaling from &gt; SPM design 5. Save output to .mat file The resulting .mat file contains five variables, Y (72x90 double), Yvar(72x90 double), block_rows (1x3 cell), descrip (lists ROIs), info (1x1 struct), regions(1x90 cell), and sumfunc('mean'). Would anyone be able to tell me exactly how to replicate this output using command line and/or a script? Your help would be much appreciated. Thanks in advance, Anna ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d </pre> azamm< at >bidmc.harvard.edu 2012-02-08T19:48:32 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1457 <pre> What is the difference between building and ROI and importing one? Why are there the two function with seemingly similar themes but very different results? </pre> zxcv 2012-02-06T11:23:08 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1454 <pre>Hi all, I'm working on a utility script to enumerate all the clusters in an arbitrary .nii file (most likely binarised) and get the centers of mass and volume for each of them. It looks like marsbar has the necessary tools. Step one is loading the .nii file, which is where I am stuck: file_root='/path/to/file'; thisvolfilename = 'filename.nii'; vol_file = fullfile(file_root, thisvolfilename); fname=vol_file %load the volume IMG = maroi_image(fname); executing the snippet (using real file names in a real filesystem): fname = /mnt/ldata/Seimens/language/crossmodal/ROIS/LFG.nii ??? Warning: Struct field assignment overwrites a value with class "char". See MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As Structures Displays Warning for details. &gt; In maroi_image.maroi_image at 34 In getcom at 29 ??? Undefined function or method 'spm_get' for input arguments of type 'char'. Error in ==&gt; my_roifname at 22 roifname = spm_get('cpath', roifname); Error in ==&gt; maroi.maroi at 133 o = my_roifname(varargin{:}); Error in ==&gt; maroi_image.maroi_image at 56 pparams.source = maroi('filename',pparams.vol.fname); Error in ==&gt; getcom at 29 IMG = maroi_image(fname); What is the syntax I should be using for maroi_image? The API suggests it should be a filename, which I assume would have to be a string. Or is marsbar able to write, but unable to read .nii files? Thanks, Chris </pre> Chris McNorgan 2012-02-02T17:32:53 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1453 <pre> to ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d </pre> valentina-fin< at >libero.it 2012-02-02T10:29:21 http://comments.gmane.org/gmane.comp.graphics.spm.marsbar/1452 <pre> ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d </pre> valentina-fin< at >libero.it 2012-01-25T10:48:27 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.graphics.spm.marsbar