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From: Nikola Valchev <n.valchev@me...>  20100929 17:10:10

Lots of different ones some positive some negative. I can also try with random numbers or my original weighted roi which has numbers between 0 and 1 (although the sum is equal to 1). Thank you for the quick answer. Nikola On Wed, 20100929 at 10:05 0700, Matthew Brett wrote: > Hi, > > > So as I understand if I ask MARSBAR to compute a simple mean from my roi > > it will give me a mean as if my roi was binary and if I ask it to give > > me a wtmean then it will give me the weighted mean. So I did and I > > checked with two rois identical in size and position but different in > > their values for each voxel. One was binary and the other had different > > integers instead of the ones. I run the batch and ask for a 'wtmean' > > instead of 'mean' as a summary function. Then when I look in the > > statistics the "t statistic" is the same... > > Ah  the 'wtmean' stuff has not been very well tested. For the ROI > with 'integers' instead of ones, were they all the same integer > (instead of 1s) or lots of different integers? If they were all the > same, then the tstatistic will be the same, because you've just > scaled the data by a constant, and thence the signal to noise hasn't > changed... > > Best, > > Matthew 
From: Matthew Brett <matthew.brett@gm...>  20100929 17:05:47

Hi, > So as I understand if I ask MARSBAR to compute a simple mean from my roi > it will give me a mean as if my roi was binary and if I ask it to give > me a wtmean then it will give me the weighted mean. So I did and I > checked with two rois identical in size and position but different in > their values for each voxel. One was binary and the other had different > integers instead of the ones. I run the batch and ask for a 'wtmean' > instead of 'mean' as a summary function. Then when I look in the > statistics the "t statistic" is the same... Ah  the 'wtmean' stuff has not been very well tested. For the ROI with 'integers' instead of ones, were they all the same integer (instead of 1s) or lots of different integers? If they were all the same, then the tstatistic will be the same, because you've just scaled the data by a constant, and thence the signal to noise hasn't changed... Best, Matthew 
From: Nikola Valchev <n.valchev@me...>  20100929 16:51:04

I managed to find some documentation on the issue. And it says in the Marsbar documentation: The most obvious way of summarizing the values within the ROI is to take the mean. This is the default in MarsBaR. The mean can be greatly affected by outliers. If we suspect there may be outlier voxels in the ROI, the median may be more robust as a summary function. The other option offered as a summary function is the weighted mean. Usually ROIs are binary – meaning that they contain ones within the ROI and zeros elsewhere. In this case the weighted mean will be identical to the mean. However, it is possible to define ROIs which contain weighting values, where high values represent high confidence that this voxel is within the region of interest, and values near zero represent low confidence. In this situation, it can be useful to use the ROI values to weight the mean value. So as I understand if I ask MARSBAR to compute a simple mean from my roi it will give me a mean as if my roi was binary and if I ask it to give me a wtmean then it will give me the weighted mean. So I did and I checked with two rois identical in size and position but different in their values for each voxel. One was binary and the other had different integers instead of the ones. I run the batch and ask for a 'wtmean' instead of 'mean' as a summary function. Then when I look in the statistics the "t statistic" is the same... I'm a bit new to the field but how exactly the weighting of the mean works? Nikola On Wed, 20100929 at 15:34 +0200, Nikola Valchev wrote: > Hello, > I've been trying to get MARSBAR to use a ROI that is not binary and give > me a weighted average of the values in the voxels from that ROI. I found > in the maroi.m file that this should be possible but I don't seem to be > able to find how to do it. Does somebody knows? > > When I import my weighting_roi.img/hdr in marsbar to create > the ..._roi.mat file binarized is set to 1 and MARSBAR is using it as a > binary ROI, which it is not. All vallues in my roi varie are from 1 to > 0. > > > Best > Nikola > > >  > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novellsfdev2dev > _______________________________________________ > Marsbarusers mailing list > Marsbarusers@... > https://lists.sourceforge.net/lists/listinfo/marsbarusers 
From: Nikola Valchev <n.valchev@me...>  20100929 13:47:36

Hello, I've been trying to get MARSBAR to use a ROI that is not binary and give me a weighted average of the values in the voxels from that ROI. I found in the maroi.m file that this should be possible but I don't seem to be able to find how to do it. Does somebody knows? When I import my weighting_roi.img/hdr in marsbar to create the ..._roi.mat file binarized is set to 1 and MARSBAR is using it as a binary ROI, which it is not. All vallues in my roi varie are from 1 to 0. Best Nikola 
From: Matthew Brett <matthew.brett@gm...>  20100928 18:35:03

Hi, > I have tried to switch the setting to the nearest neighbour resampling, by > adding on line to my script, which now says: > marsbar('on'); > roi = maroi(fullfile(ROI_path, ROI_file)); > roi = spm_hold(roi, 0); %% set NN resampling (nearest neighbour) That looks right to me  I'm afraid I am not sure what is going on either. You can try using the 'getdata' function to diagnose what is going on: http://marsbar.sourceforge.net/apidocs/marsbar/@maroi/getdata.html Specifically: Y = getdata(roi, scan_list{i}, 'ln'); % that's little L in 'ln' will give you time courses for all the voxels in your ROI, with missing values like NaN included, and using nearest neighbor resampling. If you look at where the NaNs are coming up that may show you where the problems are. Best, Matthew 
From: Iroise Dumontheil <i.dumontheil@gm...>  20100928 10:18:15
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Hi, I have been trying to extract mean parameter estimates from fMRI contrast images using SPM5 and MarsBaR. I seem to be confronted with the same problem quite a lot of people mention on the mailing list, that is for some clusters/some subjects I get an error message that says "Warning: No valid data for roi 1". My clusters are near the edge of the brain so I thought I was having the NaN problem. I have tried to switch the setting to the nearest neighbour resampling, by adding on line to my script, which now says: marsbar('on'); roi = maroi(fullfile(ROI_path, ROI_file)); roi = spm_hold(roi, 0); %% set NN resampling (nearest neighbour) for i=1:nscans mars_y = get_marsy(roi, scan_list{i},'mean'); mars_struct = y_struct(mars_y); end But it doesn't seem to improve things at all. I have also tried loading the ROIs and saving them under a new name after having run roi = spm_hold(roi,0); but again it doesn't help. I would be grateful for any help with this, I am not sure what I am doing wrong. Thanks Iroise  Dr. Iroise Dumontheil Neuroscience Department Karolinksa Institute, Stockholm 
From: Nikola Valchev <nikola.valtchev@gm...>  20100924 15:39:20

Hello, I have a question concerning MARSBAR usage. I'm doing a ROI analysis of fMRI data but the ROIs are created in a different way. They are spheres with bigger values in the center than in the periphery, in the center the voxels have values of 1 and they gradually decrease to the periphery to 0.2. That is in order to weight the extracted signal according to the distance from the center. Everything sounds nice but my ROIs are created in SPM (imcalc) and they are nii images. When I import them in MARSBAR to create the corresponding .mat file they are binarized or at least treated as binaries. Is there a way to force MARSBAR to use them with the values as I have defined them? Best regards Nikola Valchev 
From: Matthew Brett <matthew.brett@gm...>  20100923 19:39:00

Hi, Very sorry to be so slow to reply, I didn't have internet for a while... > I use SPM on Matlab R2009a. I can start marsbar without problems, however; > whenever I try a function (i.e. viewing a Roi), the following error occurs > (see below). > ??? Undefined function or method 'spm_win32utils' for input arguments of > type 'char'. Oh  that's strange  which version of SPM do you have? Is it possible that version is not supported under matlab 2009a? Best, Matthew 
From: Matthew Brett <matthew.brett@gm...>  20100923 19:08:04

Hi, Sorry to be slow to reply. > I performed a ROI analysis with a 2 x 2 ANOVA design > (2 groups and 2conditions). For factor group: independent & > unequal variance, for factor condition: dependent & equal > variance. Rather than extracting the mean ROIvalues from > each single subject, I imported my random effects design into > Marsbar and run it using my ROIs. > > Steps: Set desing from file – Extract ROI data – > Estimate results – Statistic table > > Testing for condition effects within group using the > ANOVA model in marsbar, thestatistic table revealed the > same results as paired ttests with y values(adjusted > data,extracted from the marsbar analysis) when the analysis > was performed e.g. in SPSS. > > Testing for condition effects between groups, the > statistic table revealed results that were quite > different from results obtained with SPSS, albeit the > analysis in marsbar (statistic table) and the analysis > in SPSS yielded the same > contrast values. > > I wonder which results to report and I also would like > to know the reason for these discrepant findings. It looks as though the model that you're fitting in marsbar is different somehow from that in SPSS. When you say this: > 2 x 2 ANOVA design > (2 groups and 2conditions). For factor group: independent & > unequal variance, for factor condition: dependent & equal > variance. was that something you specified in your secondlevel SPM model, or in SPSS? How did you try and match these model parameters between SPM and SPSS? Best, Matthew 
From: Elena Pavlova <Elena.P<avlova@ki...>  20100923 12:36:10

Dear all! I’d like to compare the activations in several ROIs for two contrasts (both in comparison to Rest). If I just compare the contrasts values for each ROI will it be a right way for comparing the effect size? I also tried to find the percent signal change. I have a block design with the 10 – seconds ‘events’. The numbers, which I got for the percent signal change turned out to be negative. Do you have any ideas about what could I do wrong or what could this mean? Thanks in advance, Elena 
From: Matthew Brett <matthew.brett@gm...>  20100916 19:15:14

Hi, On Fri, Sep 10, 2010 at 8:27 AM, David ro <davidro4321@...> wrote: > Hi SPMers, > > I was trying to use marsbar in order to view an activation within an ROI. > However, when I'm trying to "extract ROI data", I'm getting the following > error: > > Design reporting : ...done > Fetching data : 1/1 ??? > Error using ==> spm_sample_vol > Cant open image file. Have you checked out the entry in the marsbar FAQ: http://marsbar.sourceforge.net/faq.html#whydoigetanerrorcantopenimagefilewhenestimatingadesign Best, Matthew 
From: Matthew Brett <matthew.brett@gm...>  20100916 19:08:23

Hi, > I recently started using Marsbar to analyze my data. I noticed that it is > not possible to compute a structural ROI on the conjunction of two > contrasts. I get separate results tables for each contrast. Is there any way > to compute ROI analyses for conjunctions using Marsbar? (This is best answered on the marsbar list I think  Cc'ed) Sorry  you want the conjunction between two contrasts in a single structural ROI? If so, then no, marsbar doesn't do that... In practice, if you want what most people mean by 'conjunction', you can just see whether both your contrasts are significant or not  see the conjunction paper series in neuroimage a few years ago... Best, Matthew 
From: Matthew Brett <matthew.brett@gm...>  20100916 18:31:54

Hi, On Tue, Sep 14, 2010 at 9:53 PM, Alison Ip <iky.alison@...> wrote: > Hi, > I am working on a fMRI study, processed with SPM5. I would like to see the % > signal change and I have set the design from a SPM.mat under the option "Set > from file". After result estimation, Marsbar recognized my design as PET > study instead of fMRI. Could you advise me what's the problem underlying > this condition? I'm not sure. If it's a random effects design that would explain it (it's no longer an FMRI design in that case). If that's not the problem, could you put a copy of your design SPM.mat say on Dropbox and let me know where it is? Thanks, Matthew 
From: Alison Ip <iky.alison@gm...>  20100915 04:53:19
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Hi, I am working on a fMRI study, processed with SPM5. I would like to see the % signal change and I have set the design from a SPM.mat under the option "Set from file". After result estimation, Marsbar recognized my design as PET study instead of fMRI. Could you advise me what's the problem underlying this condition? Thanks a lot. Alison. 
From: Janelle B <beadlej@br...>  20100913 15:10:17

Hi Matthew, I have question similar to Boris.' For the GLM analysis I conducted in SPM I found that a particular brain area responded with greater magnitude to condition A than condition B or C. However when I looked at this region of interest utilizing the marsbar method I found that instead condition C showed a greater % signal change than either A or B. When examining the graphs in marsbar, it appeared that Condition C showed the greatest hypopolarization followed by condition B and then A. Could I be finding the reverse result because it is hypopolarized? I'm not quite sure how to interpret this finding. thanks, Janelle Matthew Brett wrote: > > Hi Boris, > >> I calculated the % signal change in the hippocampus using marsbar. >> >> For some condition I found a negative signal change which I interpreted >> as >> deactivation… Is this correct? >> >> How is the percentage signal change calculated? > > Did you find the FAQ entry: > > http://marsbar.sourceforge.net/faq.html#percent_signal > > There are various ways of calculating the percent signal change  see: > > http://marsbar.sourceforge.net/docdevel/latest/marsbar/@mardo/private/pr_ev_diff.html > > Once we have the curve of the fitted time course divided by the > session mean, the default method is to return the maximum from this > curve if abs(max) > abs(min), and the minimum otherwise. > > Best, > > Matthew > >  > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys  and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Marsbarusers mailing list > Marsbarusers@... > https://lists.sourceforge.net/lists/listinfo/marsbarusers > >  View this message in context: http://old.nabble.com/calculationofthepercentagesignalchangevaluetp8296861p29699341.html Sent from the MarsBaR mailing list archive at Nabble.com. 
From: Jale Özyurt <jale.oezyurt@un...>  20100913 13:30:18

Dear Matthew, dear list members, I performed a ROI analysis with a 2 x 2 ANOVA design (2 groups and 2conditions). For factor group: independent & unequal variance, for factor condition: dependent & equal variance. Rather than extracting the mean ROIvalues from each single subject, I imported my random effects design into Marsbar and run it using my ROIs. Steps: Set desing from file – Extract ROI data – Estimate results – Statistic table Testing for condition effects within group using the ANOVA model in marsbar, thestatistic table revealed the same results as paired ttests with y values(adjusted data,extracted from the marsbar analysis) when the analysis was performed e.g. in SPSS. Testing for condition effects between groups, the statistic table revealed results that were quite different from results obtained with SPSS, albeit the analysis in marsbar (statistic table) and the analysis in SPSS yielded the same contrast values. I wonder which results to report and I also would like to know the reason for these discrepant findings. Thank you very much in advance! Best wishes Jale 
From: Abela Eugenio HCAREKSSGNL <Eugenio.A<bela@ks...>  20100908 10:59:03
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Hi I use SPM on Matlab R2009a. I can start marsbar without problems, however; whenever I try a function (i.e. viewing a Roi), the following error occurs (see below). Thanks for any help Eugenio Error message: ??? Undefined function or method 'spm_win32utils' for input arguments of type 'char'. Error in ==> spm_get at 1738 drivestr = spm_win32utils('drives'); Error in ==> spm_get at 507 uicontrol(F,'Style','PopUp','Tag','DrivesPopup',... Error in ==> spm_get at 732 if isempty(F), F=spm_get('CreateFig'); end %Create SelFileWin Error in ==> spm_get at 361 [F,cF] = spm_get('Initialise','on',n,char(Prompt),Filter,NewWDir); Error in ==> mars_display_roi at 27 roi_obj = spm_get([0 Inf],'*roi.mat','Select ROI(s) to view'); Error in ==> spm at 968 evalin('base',CBs{v1}) ??? Error while evaluating uicontrol Callback 
From: Matthew Brett <matthew.brett@gm...>  20100907 12:55:50

Hi, > Marsbar calculates the mean signal from all voxel time courses in the ROI. > Is there a way to extract standard deviations or confidence intervals, too? Yes, but you'd have to get out the raw timecourses first, as in (untested): roi_obj = maroi('my_roi.mat'); design_obj = mardo('SPM.mat'); data = getdata(roi_obj, images(design_obj)); (time by voxels array) Best, Matthew 
From: Abela Eugenio HCAREKSSGNL <Eugenio.A<bela@ks...>  20100907 12:11:58
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Dear Marsbar Users Marsbar calculates the mean signal from all voxel time courses in the ROI. Is there a way to extract standard deviations or confidence intervals, too? Thanks in advance for any advice! Best regards, Eugenio Abela Clinical Research Fellow Neurology / Neuroradiology Cantonal Hospital St. Gallen / University Hospital Bern 
From: Abela Eugenio HCAREKSSGNL <Eugenio.A<bela@ks...>  20100907 12:09:20
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Dear Marsbar Users Marsbar calculates the mean signal from all voxel time courses in the ROI. Is there a way to extract standard deviations or confidence intervals, too? Thanks in advance for any advice! Best regards, Eugenio Abela Clinical Research Fellow Neurology / Neuroradiology Cantonal Hospital St. Gallen / University Hospital Bern 
From: Matthew Brett <matthew.brett@gm...>  20100902 19:22:00

Hi, On Mon, Aug 30, 2010 at 10:42 AM, Meredith Addicott <merideth.addicott@...> wrote: > I have not used Marsbar before, but would like to quantify gray matter > cerebral blood flow from MRI PASL images. I am using SPM8 to segment > individual's T1 anatomical images into gray matter masks. How do I apply > these masks onto the CBF images to get an average gray matter value using > Marsbar? What design do I specify? Maybe Marsbar isn't the best tool for you here. Probably you want to do something like erode the gray matter definition to try and take the graywhite edges off, and then use simple image multiplication and summing to get the average gray matter value. By image multiplication I mean something like: gray_mask_vol = spm_vol('gray_mask.img'); asl_vol = spm_vol('asl_image.img'); gray_img = spm_read_vols(gray_mask_vol); asl_img = spm_read_vols(asl_vol); gray_vals = asl_img(gray_img > 0.5); % where 0.5 is your ingray threshold mean_val = mean(gray_vals); See you, Matthew 
From: Matthew Brett <matthew.brett@gm...>  20100902 15:42:31

Hi, > I was extracting ROI data and got an error. > > In maroi.get_marsy at 100 > In marsbar at 918 > In ..e > ??? Error using ==> class > Out of memory. Type HELP MEMORY for your options. > Error in ==> marsy.marsy at 312 > o = class(pparams, myclass); > Error in ==> maroi.get_marsy at 114 > marsY = marsy(r_data, r_info, s_info); > Error in ==> marsbar at 918 > marsY = get_marsy(o{:}, VY, sumfunc, 'v'); > Error in ==> spm at 1276 > evalin('base',CBs{v1}) > ??? Error while evaluating uicontrol Callback. > > Can you please help me with this? I guess you have a large ROI. You may well need to reduce the size of the ROI and / or sample the data with larger voxels to reduce the number of voxels in the ROI. You will probably get a little further if you read the data in with the lower level routines, something like: roi_obj = maroi('my_roi.mat'); design_obj = mardo('SPM.mat'); img_vols = get_images(design_obj); [data vals vXYZ mat] = getdata(roi_obj, img_vols); mean_data = mean(data, 2); mY = marsy(mean_data); but if that runs out of memory too  there isn't much you can do but try and drop the memory requirements somehow... Sorry about that. Best, Matthew 
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