http://permalink.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://permalink.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 -----------------------------</pre> Yansong 2012-05-25T10:04:26 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1504 <pre> of the MarsBaR extract "percent signal change" script.  My goal is to run the script so I can extract percent signal change from multiple ROIs at once.  Error:??? Error using ==&gt; maroi.maroi at 136Use cell form of call to load multiple objectsError in ==&gt; Marsbar_percent_signal_change at 17R  = maroi (roi_file);Extract Mean Percent Signal Change script.  Problem indicated with comment.  1) make sure you have imported your ROIs from WFU and saved them % 2) make sure you have spm and MarsBaR open and running SPM.mat');D = mardo(spm_name);% below is the automatic directory method % spm_name = HC% HC = '/media/HC/HC0012_01_IM/CFNL0000000166/ep2d_Encode_0004/SPM.mat'% extract ROI dataroi_file = spm_select(2, 'mat', 'Select ROI ');R  = maroi (roi_file);         %       / \ %        |% ABOVE IS THE STEP THAT IS CAUSING MY PROBLEM % Fetch data into marsbar data objectY  = get_marsy(R, D, 'mean');% Get contrasts from original designxCon = get_contrasts(D);% Estimate design on RO</pre> Veda 2012-05-23T05:08:15 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1503 <pre>Hi, Matthew and Binu, Thank you for your answers! Yan -----Original Message----- From: Matthew Brett [mailto:matthew.brett&lt; at &gt;gmail.com] Sent: Tuesday, May 01, 2012 12:57 PM To: MarsBaR users list Subject: Re: [Marsbar-users] Percent signal change calculation Hi, On Fri, Apr 27, 2012 at 7:38 PM, Binu Thomas &lt;binu.thomas&lt; at &gt;utsouthwestern.edu&gt; wrote: To add to Binu's answer - the percent signal change calculation is 1) - reconstruction of the event time course as you have modeled it 2) take a measure of that time course as the amount the signal has changed (the measure is usually the max difference from baseline, +ve if the max is &gt; the min, -ve otherwise) 3) Divide that measure by the mean signal across the whole run in the ROI So, if you add a temporal derivative, this can change the estimated shape of the HRF, and so the signal change, but it will not change (much) if in fact your event is more or less canonical HRF shape. Whether the implicit baseline is important is a little difficult to say. I gene</pre> Yan Fang 2012-05-01T22:02:50 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1502 <pre>Hi, On Fri, Apr 27, 2012 at 7:38 PM, Binu Thomas &lt;binu.thomas&lt; at &gt;utsouthwestern.edu&gt; wrote: To add to Binu's answer - the percent signal change calculation is 1) - reconstruction of the event time course as you have modeled it 2) take a measure of that time course as the amount the signal has changed (the measure is usually the max difference from baseline, +ve if the max is &gt; the min, -ve otherwise) 3) Divide that measure by the mean signal across the whole run in the ROI So, if you add a temporal derivative, this can change the estimated shape of the HRF, and so the signal change, but it will not change (much) if in fact your event is more or less canonical HRF shape. Whether the implicit baseline is important is a little difficult to say. I generally use implicit baselines myself (by which I mean unmodeled baseline tasks). If you have no implicit baseline, and therefore all the time of the run is covered by events in your model, then you can run into a situation where the sum of the event regressors i</pre> Matthew Brett 2012-05-01T17:56:36 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1501 <pre>I don't think the implicit baseline will affect your percent signal change, but having modeled both time and dispersion derivative can lower your percent signal change, as the signal is being split into both time and dispersion derivative bins. Area under the curve calculation can be used as an alternative ROI method. Binu ________________________________ From: Yan Fang [yan.fang&lt; at &gt;utsouthwestern.edu] Sent: Friday, April 27, 2012 6:09 PM To: marsbar-users&lt; at &gt;lists.sourceforge.net Subject: [Marsbar-users] Percent signal change calculation 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. --------</pre> Binu Thomas 2012-04-28T02:38:56 http://permalink.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/listinf</pre> Yan Fang 2012-04-27T23:09:56 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1499 <pre>Hi, On Wed, Apr 25, 2012 at 5:54 AM, Chaleece Sandberg &lt;challysand&lt; at &gt;gmail.com&gt; wrote: No, I'm afraid there isn't an easy way to get individual event timecourses in Marsbar, unless you enter the individual events as their own condition, and use FIR as the basis function. If you do that you will probably find it is incredibly noisy - of course you now only have one scan per point in your time course. But from the later part of your email I wonder whether you just want some sort of single HRF estimate per event? In that case you'd still need one condition per event, but you could use an HRF basis function. That would give you several scans to stabilize the signal for the event. Best, Matthew ------------------------------------------------------------------------------ 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 </pre> Matthew Brett 2012-04-27T17:47:22 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1498 <pre>Great, thanks! One more question for this thread. I've been digging a bit, but can't seem to find what need. It's possible I just don't know enough to recognize the name of what I'm looking for. I see in the FAQ that I can get the raw timecourse in a specific ROI for the entire run. Is there any way to extract that data for each event of one condition within a run if the design is event-related? It's a bit messy trying to align the conditions against the timecourse, especially since my timing is not in multiples of the TR. For example, I have 50 randomized events of condition A within a run and would like to have a list of 50 raw signal values within a specific ROI representing each time condition A was presented (rather than the average, which would be the % signal change, correct?). Thanks, Chaleece ---------- Forwarded message ---------- 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, 23 Mar 2012 12:31:27 -0700 Subject: Re: [Marsba</pre> Chaleece Sandberg 2012-04-25T12:54:07 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1497 <pre>Hi Matthew I have a quick question about post hoc manipulation of contrast value data. Is it valid to take the mean contrast value across a group of ROIs from a putative network (say, the default mod network), to show that the regions of a network are more or less active across a group level in a given task? Thanks Mac ------------------------------------------------------------------------------ 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> Mac Shine 2012-04-25T03:32:44 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1496 <pre>Hi, On Tue, Apr 24, 2012 at 3:00 AM, Ming-Tsung Tseng &lt;d93421007&lt; at &gt;ntu.edu.tw&gt; wrote: The first one is the % signal change, the second one is just the contrast (combination of beta) values. If you have just one HRF regressor for your condition and just one session then the % signal change = beta_event_1 * regressor_event1_max_height / session_baseline, where 'regressor_event_1_max_height' is a reconstructed regressor for and event of the duration you asked for. So the signal change is just the beta times a scale factor. If this scalefactor is the same for your two events, then the contrast value (beta2 - beta1, say) will be the same as the subtraction of the percent signal change times a scale factor. Best, Matthew ------------------------------------------------------------------------------ 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, mobi</pre> Matthew Brett 2012-04-24T16:55:44 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1495 <pre>Hi, On Tue, Apr 24, 2012 at 7:47 AM, Andrew Furman &lt;afurman3&lt; at &gt;jhu.edu&gt; wrote: Yes, although it would be odd to specify things like global scaling. You mean - what numbers are in the contrast image? They are linear combinations of the betas. If you had a design matrix with 2 conditions, and the first two columns were an HRF regressor for condition 1 and condition 2, and your contrast was [-1 1 0 0 ... ], then the resulting contrast image is an image of the beta_0002.nii - beta_0001.nii . Best, Matthew ------------------------------------------------------------------------------ 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> Matthew Brett 2012-04-24T16:42:34 http://permalink.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://permalink.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 </pre> CarlosTseng 2012-04-24T01:58:24 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1492 <pre>Hi, I wanted to update that the suggestion worked! I only needed to add another code line in the maroi_pointlist.m to round the coordinates before they're being checked for integers so that it'll succeed. Thanks! Sharon Gilaie-Dotan On Thu, Apr 19, 2012 at 9:42 AM, Sharon Gilaie-Dotan &lt;shagido&lt; at &gt;gmail.com&gt;wrote: </pre> Sharon Gilaie-Dotan 2012-04-19T19:55:11 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1491 <pre>Matthew hi, thanks. yes the list of coordinates are integers and they are from a 1mm spaced space. i will try your solution and update if it works. Best wishes and thanks again Sharon On Apr 19, 2012 9:33 AM, "Matthew Brett" &lt;matthew.brett&lt; at &gt;gmail.com&gt; wrote: ------------------------------------------------------------------------------ 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> Sharon Gilaie-Dotan 2012-04-19T06:42:49 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1490 <pre>Hi, On Wed, Apr 18, 2012 at 10:16 PM, Sharon Gilaie-Dotan &lt;shagido&lt; at &gt;gmail.com&gt; wrote: Thanks for posting. This might be a little difficult. Do you happen to know if the MNI coordinates are from voxels? I mean, are they integers? Are they exactly 2mm apart or 1mm apart at closest? The trick will be to read them into a matlab array with something like: vals = spm_load('my_coordinates.txt'); And then you need an affine matrix from an example MNI image: pth = spm('dir'); fname = fullfile(pth, 'templates', 'T1.nii'); affine = spm_get_space(fname); Then something like: params = struct('XYZ', vals', 'mat', affine); % note vals' should be 3 by N roi = maroi_pointlist(params, 'mm'); saveroi(roi, 'my_roi.mat'); That might work (I haven't tested it)... Best, Matthew ------------------------------------------------------------------------------ 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:/</pre> Matthew Brett 2012-04-19T06:33:11 http://permalink.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://permalink.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://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1487 <pre>Hi, On Tue, Mar 6, 2012 at 5:13 AM, Chaleece Sandberg &lt;challysand&lt; at &gt;gmail.com&gt; wrote: Sorry to take so long to reply. I think the authors there are just referring to the use of effect sizes that aren't divided by their standard deviation. In the SPM and marsbar these would be the 'beta' or 'contrast' values. Also the marsbar percent signal change is raw rather than standardized in that sense, Best, Matthew ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure </pre> Matthew Brett 2012-03-23T19:31:27 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1486 <pre>Hi, On Wed, Mar 7, 2012 at 6:48 AM, Su, Merina &lt;merina.su.10&lt; at &gt;ucl.ac.uk&gt; wrote: I'm afraid you'd have to take the ROIs, export them as images, apply the normalization parameters to the images, then re-import them. I wouldn't do that though - you can just use the ROIs as they are; marsbar will deal with the differences in voxel size. The explicit mask just stops SPM analyzing anything outside the ROI. You'll get SPM results (t maps etc) for just the voxels in the ROI. The extract data option gets the raw data out of the ROI for you to play with, and doesn't do any statistics on the data. Best, Matthew ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure </pre> Matthew Brett 2012-03-23T19:24:49 http://permalink.gmane.org/gmane.comp.graphics.spm.marsbar/1485 <pre>Hi, On Tue, Mar 13, 2012 at 8:30 AM, Jessica Wojtalik &lt;jesswojo1&lt; at &gt;gmail.com&gt; wrote: Sorry for the slow reply, thanks for the nice words. Yes, exactly. Yes, if that's your only test, it would be reasonable to use 0.05 as a threshold. I wasn't sure what you were trying to test? It would be 40 if you want the percent signal change during the block compared to rest. I hope that's useful, sorry again for the slow reply, Best, Matthew ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure </pre> Matthew Brett 2012-03-23T19:20:19 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.graphics.spm.marsbar