gmane.comp.graphics.spm.marsbar

Marsbar doesn't recognize analyze images (spm5)

Igor_ — 2008-12-03T15:20:43

Dear Matthew, dear users, i have a basic question on using Marsbar under spm5. First, I couldn’t run Marsbar at all, then I downloaded spm5 files from https://svn.sourceforge.net/svnroot/marsbar/trunk/marsbar/spm5/ Afterwards, I could run Marsbar, but I can not download binary images (in analyze format) for creation of a VOI (option "import"). Specifically, Marsbar seems to not recognize analyze images at all. Do I need to download any other additional matlab files to resolve this problem? Sorry for such a simple (stupid?) question – I, as a simple physician, have unfortunately no idea from programming or matlab.. Thanks in advance. Igor

Re: Base space for ROI & Coordinate in millimeters

romain valabregue — 2008-12-03T09:48:47

Hello, I do not see a particular reason to save milimeters or image space coordinate. The important feature is to save the volume dimention an orientation which were used to define the roi. In this way you can get the roi in any other space. (and you can also the milimeter position) roi_o = maroi('roiname.mat') V = spm_vol('path_to_the_volume_you_want_to_put_the_roi_in') sp = mars_space(V); Pos = voxpts(roi_o,sp); Pos will contain the coordinate in pixel space of the new image. I hope this help Jaime Shinsuke Ide a écrit : ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

Re: roi values

romain valabregue — 2008-12-03T10:09:10

hello you can get the milimetric value of the roi point. If your roi has been defined in a volume which is in the MNI space then you'll get the coordinates in MNI space ... roi_o = maroi('roiname.mat') sp = native_space(roi_o); %gives you the space of the image where the roi was define Pos = voxpts(roi_o,sp); Pos will contain the coordinate in pixel space. to converte it in milimeter : Posmm = sp.mat(1:3,1:3)*Pos + repmat(sp.mat(1:3,4),1,size(Pos,2)); I hope this help Romain Jac501 a écrit : ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

roi values

Jac501 — 2008-11-30T18:49:36

Dear users, Sorry, I've serched the forum and can't find an obvious answer to this. How do I extract roi x y z coordinates in MNI, or even better Tal space? I'm not interested in any stats, just cordinates for binary roi's to use with another program. At the moment I can on get centre of gravity from the .mat file. Thank you in advance. JB

Re: marsbar installationHi,

Matthew Brett — 2008-11-28T04:18:42

Hi, This is not a path problem, but it means for some reason that your ROI is empty (trying to combine ROIs, etc). What is the ROI that you are defining that is empty? Best, Matthew ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

Re: marsbar installationHi,

Danielle van Westen — 2008-11-27T20:57:20

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Re: Base space for ROI & Coordinate in millimeters

Jaime Shinsuke Ide — 2008-11-27T17:33:15

Re: marsbar installationHi,

Matthew Brett — 2008-11-27T16:17:59

Hi, On Wed, Nov 26, 2008 at 12:41 PM, Danielle van Westen med.lu.se> wrote: You just need to: add the marsbar root folder (the folder containing marsbar.m) to the matlab path (and _not_ the subfolders). run at the matlab prompt. This will set the paths correctly for you, and all functions should work after that... Best, Matthew ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

marsbar installationHi,

Danielle van Westen — 2008-11-26T20:41:03

Base space for ROI & Coordinate in millimeters

Jaime Shinsuke Ide — 2008-11-26T18:31:01

ROI creation

Danielle van Westen — 2008-11-25T07:06:37

Re: MarsBar batch to get residuals

RRoman — 2008-11-17T13:00:07

I think the next is more likely to be correct: D = mardo(spm_get); % specify SPM.mat mY = get_marsy(R, D, 'mean'); E = estimate(D, mY) residuals = residuals(E); the timecourses ectracted using this script look very similar to the ones I get using SPMd but not the same (e.g. correlation coefficient is around 0.95-0.97). I don't understand what bit I'm missing as both toolboxes seem to be using SPM mashinery to calculate the residuals ... would be realy great to learn (even suggestions would be great) Thanks, Roman RRoman wrote:

MarsBar batch to get residuals

RRoman — 2008-11-15T17:49:47

Hi Matthew, I've seen the script you wrote in response to a question from Michiru. Tried to adopt for what I need (extraction of residuals from an ROI). The result is different from what I get using MarsBar GUI. Could you please advise what is wrong here. D = mardo('SPM.mat'); mY = get_marsy(R, D, 'mean'); E = estimate(D, mY) Y = summary_data(mY); SPM = des_struct(E); ifX = SPM.xX.pKX; B = betas(E); fitted = ifX * B; resid = Y - fitted; Thanks in advance, Roman

re siduals using MarsBar and SPMd

RRoman — 2008-11-15T17:12:26

Hi Matthew, I extracted residuals from ROIs using Marsbar and SPMd to see the difference. They are different. I wander if I'm doing anything wrong in Marsbar? 1. design matrix contains confounds to be removed and an empty regressor 2. in Marsbar: extract mean timcourses for ROIs ("Extract ROI data"); estimate results ("Estimate Results"); obtaining timecourse for the residuals: "MarsBar SPM Graph"; any contrast for empty regressor; "adjusted"; looking at variable y in the workspace Obtaining residuals in SPMd is pretty straigtforward: "Scan Details" in SPMd; extracting mean timecourses for the ROIs using "Extract ROI data" in MarsBar. Could you please help? Thanks, Roman

Re: residual time series after FIR model fitting

Matthew Brett — 2008-11-08T21:15:50

Hi, As for SPM, this is not straightforward. The data and the design are filtered before estimation, so you will have to replicate this, to get the filtered residuals (these are the residuals from the model SPM and marsbar uses). This involves Run the estimation with FIR modeling of the events D = mardo('SPM.mat'); mY = get_marsy(R, D, 'mean'); E = estimate(D, mY) Filter the time course with the design filter -> fY Y = summary_data(mY); fY = apply_filter(E, Y); Get the inverted filtered design matrix (ifX = pinv(fX), where fX is the filtered design matrix) from the SPM structure: SPM = des_struct(E); ifX = SPM.xX.pKX; Get the betas from the original estimation: B = betas(E); Get the filtered residuals -> fR: fitted = ifX * B; fR = fY - fitted; I think that should work. Best, Matthew ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK

residual time series after FIR model fitting

Michiru Makuuchi — 2008-11-08T20:50:28

Hi, I like to obtain residual time series after FIR model fitting to calculate functional connectivity. Could you tell me how I can do this by batch? Thank you in advance! Michiru ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

Re: a problem with 'get_marsy'

Matthew Brett — 2008-11-08T20:04:54

Hi, That's very strange. get_marsy is a method of the 'maroi' class, so it should be called as a result of the 'R' object in your script. What type of thing (>> whos) is 'R' in your script, after you've run it? Best, Matthew ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

Re: time-course / % change

Matthew Brett — 2008-11-08T20:01:21

Hi, First - I am sure you found this, but there's an item in the FAQ explaining how the % signal change is calculated. After that, you will need the code itself, which is in http://marsbar.sourceforge.net/doc-devel/latest/marsbar/< at >mardo/event_signal.html No, the fitted events use the usual SPM scaling units. They will be a bit similar to % signal change, but not the same. No, I don't think so. The model of the time course should be the same for the two calculations - in fact the % signal change uses the fitted event calculation. Right... The easiest way is use marsbar to calculate the % signal change, as it used the fitted time course. If you want to see how it's done, read the FAQ entry, and compare it to the code in the routine above, you'll see that we use the event_fitted time course to calculate the % signal change, but they are not the same. In essence it's (lines 51 - 60 of event_signal) Get the fitted time course. Get something like the abs(max) of the fitted time course- see http:/

a problem with 'get_marsy'

Michiru Makuuchi — 2008-11-08T19:38:52

Hi, I got an error message as follows when I tryed to extract time course. ??? Undefined function or method 'get_marsy' for input arguments of type 'mardo_5'. The following is the script. D = mardo(spm_name); R = maroi(roi_file); Y = get_marsy(R, D, 'mean'); How can I solve this problem? I am using matlab 7.6.0. Thank you in advance! Best regards, Michiru ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/

time-course / % change

Vaughn R. Steele — 2008-11-08T19:37:01

Hello All, I've run into something I can't seem to figure out, even with the FAQ and the mailing list. Perhaps I missed something. In any case, I hope these are simple enough questions to be answered easily. - We used MarsBaR to extract % signal change and time courses (fitted event) from several ROIs within out data. When we look at the % change numbers and the time course numbers, they don't match up. - Shouldn't the peak (abs max) time course be our peak % change too? - In an e-mail reply on the mailing list, it was suggested that perhaps the time course is calculated with one HRF and sometimes the percent change is calculated with another (e.g. from the SPM estimate). Could this be the reason why our % change and time course peaks aren't the same? - Or, are the differences in these numbers due to the 'SPM units'? Is it that one of these measures (time course or % change) is in 'SPM units' and the other is not? If so, how can we convert one into the other? - We also have been trying t

FIR values

Karuna Subra — 2008-10-29T02:41:35

Hi all, Does anyone know what the matlab prompt is to get the actual FIR value of an individual subject's hrf at each time-point? I am able to plot out the FIR graph but not get the actual values to export to a spreadsheet. Thanks! Karuna Karuna Subra Postdoctoral Fellow Vinogradov Lab UCSF ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/