Joshua Gertler posted a comment on discussion Open Discussion

Hi All, I am having an issue where marsbar says that the roi file is empty, and changing the spm hold to 0 doesn’t help. When I create ROIs from clusters it creates the .mat file, but when I go to view the ROI with marsbar it is unable to view it because it says the file is empty. This is what the roi.mat file says: val = [maroi_pointlist - Emo_Neu cluster at [41.7 21.6 -9.9]] label: 'Emo_Neu_42_22_-10' source: '/blue/camctrp/working/jgertler/MisoPilot/BIDStest/derivatives/sub-18/func/MARS/Emo_Neu_42_22_-10_roi.mat'...

S M posted a comment on discussion Help

Hello, Background : I'm currently running a study in which I wish to examine the effects of cognitive training on brain activity across time, in pre-selected specific ROIs. I have 3 cognitive training groups and 3 timepoints (therefore 3 fMRI scans per participant that each represent a different timepoint). Problem : Using MarsBar, I am extracting parameter estimates (betas) within specific ROIs from pre-existing One T-tests done in SPM. However, when extracted, I noticed that the values change slightly...

Narges created ticket #8

What do extracted values from ROI signify?

Narges posted a comment on ticket #7

Hi Matthew, Thanks for letting me know! I've just posted my question to the https://marsbar.discourse.group/. Regards, Narges

Matthew Brett posted a comment on ticket #7

I'm sorry - I'm hardly using this forum - would you mind posting over at https://marsbar.discourse.group/ ?

Narges created ticket #7

voxel dimensions_ROI extraction in Marsbar

Matthew Brett posted a comment on discussion Open Discussion

I'm really sorry I missed this one. If you still haven't solved this - can you post over at https://marsbar.discourse.group/ ?

Matthew Brett posted a comment on discussion Help

Ah - sorry - I should have said - we've moved now, to https://marsbar.discourse.group/ - could you post again there? I'll reply as soon as I can.

MarsBaR ROI toolbox for SPM released /README.md

MarsBaR ROI toolbox for SPM released /README

MarsBaR ROI toolbox for SPM released /README.md

Sejal Ghate posted a comment on discussion Help

Hi Dr. Brett, We are currently working on a project to analyze PET scans of Alzheimer's' disease subjects acquired from a longitudinal multi-site study. I was looking at the Marsbar tutorials as a tool to perform ROI extraction. Currently, we are aiming at analyzing only one of our subjects - I tried inserting the specific subject into the ROI extraction program, but it asks for a SPM.mat design file. This design file would correspond to some type of statistical analysis carried out between subject...

Ann Zach posted a comment on discussion Help

Hi all, This is the first time I am using MarsBaR and I need some help. I am trying to batch script roi extraction from nifti files (GM, WM and CSF segmentations). I have the following lines: ... roifiles = dir(sprintf('%s/mri/pnii', folder)); % pnii are the GM, WM and CSF segmentation files generated by spm GMseg = roifiles(1).name; WMseg = roifiles(2).name; CSFseg = roifiles(3).name; marsbar('on'); GMroi = maroi_image( GMfile); WMroi = maroi_image(WMfile); CSFroi = maroi_image( CSFfile); I am getting...

wangmuke posted a comment on discussion Help

Hi, I have a question about the extract ROI data. For example, for the PPI based neural activity extraction, are there any differences between the values extracted by Marsbar Full Option and SPM Eigenvariate?

Gargi Majumdar posted a comment on discussion Help

Hi all, I am trying to extract the time-series for all the ROIs for whole-brain.. I have performed following steps: 1. Using the GUI, set design - SPM.mat file (for 1 subject) 2. Data - Extract ROI data (full options) - selected 246 ROIs 3. Scale grand mean - 0 4. I got the Summary of the ROI data After that when I am trying to Estimate results, the following error is displayed: Out of memory. Type "help memory" for your options. Error in pr_estimate (line 219) q = diag(sqrt(trRV./ResSS'),0); % spatial...

ilaria sani posted a comment on ticket #6

My apologies! I thought they were the same thing. Thanks for catching this promptly. Best, Ilaria Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.eduhttps://rumail.rockefeller.edu/owa/redir.aspx?C=Kqhy3ohui0OLc6NBHS0gx_jC9yHmUtEIuvMTV8kpl1lEP6utIV_5LPRr35l0-k2eSQyLqrMn4XI.&URL=mailto%3assadagopan%40rockefeller.edu From: Matthew Brett matthewbrett@users.sourceforge.net...

Matthew Brett posted a comment on ticket #6

Sorry - I'm afraid I don't monitor this forum. Could you post to the mailing list instead? Cheers, Matthew

ilaria sani created ticket #6

unable to buid roi from image (batch)

ilaria sani posted a comment on discussion Open Discussion

I thought I had found a workaround by using fname = spm_vol(roi_list{i1}); % instead of fname = 'image.nii' roi = maroi_image(fname); roi = maroi_matrix(roi); the script now runs without errors and roi.mat is generated. However, when I attempt to visualize the rois from marsbar - roi definition - view They do not appear in the gui in the folder where they are. Thus I understand that marsbar does not recognize them. Does anyone have a clue? I noticed that the there is one difference between the roi...

ilaria sani posted a comment on discussion Open Discussion

Dear All, I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects. I am using the example lines provided: fname = roi_list{1}; roi = maroi_image(fname); I get an error early on while loading the roi. I have seen a couple of posts that resolved a similar issue by adding marsbar('on'). It didn't work for me. I tried to versions of matlab: 2016b and 2019a - same error I am using spm8 I am able to use the line params.vol = spm_vol(params)...

Valérie D'Amour-Horvat posted a comment on discussion Help

Hello, I find myself a bit confused as to which function I should use to combine two ROIs into one (for example, Left and Right Ventral Striatum). Those initial regions were derived from a number labelled mask, and as such, are not based on functional activation from my own participants. I tried both the r1 | r2 function and the r1 + r2 function, and both give me different values when I extract the beta weights for my participants. Is it because the left and right ventral striatum ROIs overlap to...

Simon Thibault posted a comment on discussion Help

Hi, I am trying to extract the time course of beta estimates in specific ROIs. However I have some issues to do it properly. Indeed, let's say my ROI contain 124 voxels, I should get a vXYZ matrix of 3x124 dimensions and Y matrix of n x 50. However for some ROIs I do not get n x 123 but rather n x 49 or even n x 4 depending on where is localized the ROI. What could be the origin of this problem? Best, Simon

Jamie Snytte posted a comment on discussion Open Discussion

Hi, Thank you for all your informative posts. I'm just wondering if I can use MarsBar to run a first level analysis on images native space. We're just concerned that MarsBar runs it's estimation steps through SPM, and that SPM requires images to be in MNI or a standard space. We've manually traced multiple ROIs on high resolution T2 images, and co-registered these labels to our mean functional images. Now we'd like to extract the betas and T-Values from these regions based on contrasts we're running....

Jamie Snytte posted a comment on discussion Help

Hi, Thank you for all your informative posts. I'm just wondering if I can use MarsBar to run a first level analysis on images native space. We're just concerned that MarsBar runs it's estimation steps through SPM, and that SPM requires images to be in MNI or a standard space. We've manually traced multiple ROIs on high resolution T2 images, and co-registered these labels to our mean functional images. Now we'd like to extract the betas and T-Values from these regions based on contrasts we're running....

Payal posted a comment on discussion Open Discussion

Hi I am trying to extract data using marsbar. For few ROI s I get an error "No Valid data ". I tried the fix suggested in FAQ section of MArsbar. It id not work . I also tried using getdata and I get empty matrix . I am not sure what I should do next.? I created ROI from structural image. i have also checked they are aligned with functional data and also structural data. i will be grateful if you can help me out. thank you Payal

Monica Nicoli posted a comment on discussion Open Discussion

Dear experts, I have been trying to write batch scripts to build rois from binarized nifti images. I found in previous discussion the usage of maroi_image function, but I always get the same error in line 34 of the function. I've tried the maroi_build_image function as well, but it opens the graphical window of marsbar so that I have to do it manually for every image, as I did before trying to script the process. Could you suggest me a way to write a script usign the "build image" function for several...

Jamie Snytte posted a comment on discussion Help

Hi, I am currently running a functional analysis where I want to extract the brain activity at pre-segmented ROIs. My participants images have been pre-processed (motion corrected and the structural image + segmented labels have been co-registered to the the mean EPI using SPM12). I want to run the GLM analysis on each of my ROIs and I just want to know how to visualize the results in native space. The statistics appear in the command window in Matlab, but we'd like to visualize this on the brain...

Catarina Amado posted a comment on discussion Help

Hello everyone, I have been using marsbar for a while, but I never encountered something like this. Basically, I have the following error when I try to extract the FIR time courses. The percent signal change extraction works perfectly and I also tried to extract the FIR using the GUI and also works, but I would like to have this working on a script basis. Can someone help me? Thanks in advance. Warning: Action '!ContextHelp' is deprecated. In spm_help (line 116) In pr_spm_get_bf (line 32) In mardo_2/event_x_fir...

Bahar posted a comment on discussion Open Discussion

Hello all, I have exctracted ROI for different brain regions using Marsbar, but I see no roi.matrices provided. Do you know how can I build that by having MNI coordinates and radius? I need the matric for data analysis. Any help would be greatly appreciated. Thank you.

Pradeep D posted a comment on discussion Help

Hi there, I need to report both mean and confidence interval for each ROI. Could marsBar report confidence interval for each contrast and each ROI in the "statistic table" output? I kindly request to support this feature. Thanks, Pradeep

Kaio Felippe Secchinato posted a comment on discussion Help

I'm trying to extract the percent singal change bold fmri variation by the marsbar toolbox and it's showing several errors. My version of SPM is 12. The following errors: Error using spm_sample_vol Cant open image file. Error in spm_get_data (line 44) Y(i,:) = spm_sample_vol(V(i),XYZ(1,:),XYZ(2,:),XYZ(3,:),0); Error in spm_data_read (line 48) Y = spm_get_data(V,varargin{2}); Error in spm_regions (line 181) y = spm_data_read(SPM.xY.VY,'xyz',xSPM.XYZ(:,Q)); Error using waitfor Error while evaluating...

Isabelle Tottenham posted a comment on discussion Help

Hi Expert, I am trying to extract timecourses from AAL ROI's. I have tried building my own and used the downloaded file marsbar-aal-0.2 from this site. This is the error I receive when trying to extract the data from .nii files: ??Mapping files : ...done Fetching data : 1/1 Output argument "vXYZ" (and maybe others) not assigned during call to "maroi/getdata". Error in maroi/get_marsy (line 76) [y vals vXYZ mat] = getdata(o, VY); Error in marsbar (line 990) marsY = get_marsy(o{:}, VY, sumfunc, 'v');...

sheelakumari r posted a comment on discussion Open Discussion

Hi I am trying to extract the susceptibility values of specific ROIs(say, putamen, caudate, hippocampus etc.) using MARSBAR. I created smoothed images of QSM data after segmenation. Also obtained the masks of the above mentioned ROIs from WFUPICK ATLAS. I wish to overlay the mask on QSM map to extract mean values using MARSBAR software. What are the steps I have to follow to extract the values. Please find the pasted link that mentioned the same methodology. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577408/...

Ramesh Babu posted a comment on discussion Help

Dear Expert, I have done VBM analysis using spm12. Now I would like to perform roi analysis using MaraBar. Before downloading and installing this software I would like to know whether this will work in spm12. Your information will be helpful for my research. Thanks Ramesh

boris posted a comment on discussion Open Discussion

Dear all, I found some old posts on this topic but not a real solution. I have a parametric modulation at the frst level for each subject. I would like to extract the signal changes form each subject from this parametric modulated data. Marsbar (0.44 & SPM12) only gives me the signal changes from the non-modulated regressors... Thes values do not make any sense as I contrasted the modulated data on the 2nd level... Are ther any options to extract the modluated signal changes??? Many thanks, bori...

Ceyda Sayali posted a comment on discussion Open Discussion

How does marsbar import ROIs from cluster image? What is the algorithm it implements...

Matthew Brett posted a comment on ticket #5

Sorry - I should have disabled the support request part of this site - it's rarely...

Maria Hakonen created ticket #5

Plotting time series from a ROI

Ceyda Sayali posted a comment on ticket #4

There is a discrepancy between the sizes of Y, multv and vXYZ in my case: Y: 1 by...

Matthew Brett posted a comment on ticket #4

Hi, On Wed, Aug 24, 2016 at 4:01 PM, Ceyda Sayali zceydas@users.sf.net wrote: [support-requests:#4]...

Ceyda Sayali created ticket #4

The size of voxel betas and voxel coordinates do not match

Pauline Favre posted a comment on ticket #9

and the mask

Pauline Favre posted a comment on ticket #9

Alright, so I tried to import a nii image (IN_L_conj.nii, attached) to marsbar format....

Matthew Brett posted a comment on ticket #9

I'm afraid it is necessary to have a base-space for the ROIs - that includes the...

Pauline Favre created ticket #9

modify voxel size default

Tina J posted a comment on discussion Help

Dear MarsBar Experts, I am new to Marsbar & ROI analysis, so please forgive the very...

Pauline Favre posted a comment on ticket #8

Dear Matthiew, It seems to work normally now. (Maybe a problem with the paths..)....

Matthew Brett posted a comment on ticket #8

On Thu, Aug 6, 2015 at 9:27 AM, Pauline Favre eniluapervaf@users.sf.net wrote: Hi...

Pauline Favre posted a comment on ticket #8

Hi Matthew, thanks for your reply. I attached a SPM.mat file. Best

Matthew Brett posted a comment on ticket #8

On Wed, Aug 5, 2015 at 3:38 PM, Pauline Favre eniluapervaf@users.sf.net wrote: [bugs:#8]...

Pauline Favre created ticket #8

compatibily marsbar0.44 / spm8?

Shilpi Modi posted a comment on discussion Help

Dear all, I have a MPRAGE data of 70 subjects. Using DARTEL toolbox of SPM, I have...

rocco chiou posted a comment on discussion Help

I was trying to extract data from a region of interst and kept running into this...

MarsBaR ROI toolbox for SPM released /marsbar/0.44/README.rst

MarsBaR ROI toolbox for SPM released /marsbar/0.44/marsbar-0.44.tar.gz

MarsBaR ROI toolbox for SPM released /marsbar/0.44/marsbar-0.44.zip

MarsBaR ROI toolbox for SPM released /OldFiles/marsbar-0.35.tar.gz

MarsBaR ROI toolbox for SPM released /OldFiles/marsbar-aal-0.1.tar.gz