gmane.comp.graphics.spm.marsbar

help error - Cant open image file

Hi

I’ve a problem with marsbar. This is the first time it shows me this error; I usually use marsbar without any problem.

I define a specific cluster and I write the ROI: so I obtain the xxx_roi.mat.

Then I want to extract the time series, so I open extract ROI data, select xxx_roi.mat, select the SPM.mat and the follow error is displayed:

Fetching data : 1/1 ??? Cant open image file.

Error in ==> maroi.getdata at 103

data = spm_sample_vol(data_imgs(i),...

Error in ==> maroi.get_marsy at 76

[y vals vXYZ mat] = getdata(o, VY);

Error in ==> marsbar at 975

marsY = get_marsy(o{:}, VY, sumfunc, 'v');

Error in ==> spm at 1276

evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback.

I download the tool again and I try to use it again but nothing, so what’s happened? What do I have to do?

Thank you

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jandrews | 1 Oct 18:53

% Signal Change vs. mean or baseline? ; FIR + GLM; NaNs


Hello, 
     I was hoping someone may be able to clarify for me a couple of details
about how MarsBar works that I gathered from previous postings.  Could
someone could either confirm or clarify the following statements?  

1) I think MarsBar calculates % Signal Change as change compared to the mean
of the session, NOT compared to fixation trials (or other "baseline" trials
that are not explicitly entered into the design matrix).  Is this true?  If
so, is there any option to change the way % Signal Change is calculated such
that it reflects change from fixation?

2) I believe MarsBar FIR responses must in some way interact with the SPM
GLM above and beyond simply querying the trial onsets.  I was originally
under the impression that the FIR response calculated was derived solely
from the raw data and the trial onsets.  However, when I compared MarsBar
timecourses from 2 GLMs that differed only with respect to the way the event
duration was specified (i.e. in one GLM, the event duration was set to 0s,
whereas the other was set to 2s), the MarsBar timecourses were different. 
To my understanding, if MarsBar only used the raw data and the trial onsets
to calculate the timecourses, the two timecourses would be identical.  

3) I am less clear on this last point -- how MarsBar handles NaNs.  If
MarsBar calculates timecourses within an ROI from the RAW data (smoothed
analyze SPM images), then all of my ROIs for all subjects have data within
them, because no brain mask was applied to my raw data.  However, the SPM
beta and con outputs were applied with the default brain mask, thus causing
some voxels on the edge of the brain to become NaNs.  Does this same issue
thus pertain to MarsBar?  Are NaNs simply omitted from the ROI or are they
converted to 0?  

Thanks so much for any clarification!
Best, 
Jessica

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Matthew Brett | 24 Sep 19:15

Re: [SPM] SPM5/Marsbar bug

Hi,

> Fetching data:
> Warning: No valid data for roi 1 (points_coordinate_mm_-42_-6_56)
>> In maroi.get_marsy at 80
>  In marsbar at 975
>  In spm at 857

I think you may have run into this problem:

http://marsbar.sourceforge.net/faq.html#novalid

Best,

Matthew

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KIDLAB | 24 Sep 16:00

Combining Structural ROIs


Hello All,

  I have imported my structural ROI's from wfu pickatlas, but when I try to
combine them in Transform-Combine, it seems to hang up after I enter r1 & r2
& r3, with no information as to why in the matlab window.  I waited 15
minutes, just to make sure it just taking a while, but there is still
nothing.  Can someone help?

Thanks!
KIDLAB
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federico.tubaldi | 20 Sep 22:11

Marsbar error: No valid data for roi

Dear Experts,

I am performing a ROI analysis by using marsbar. I define 5 ROIs as five
different single voxels. After setting the desing I extract the data from
each ROI. Everything works fine for 4 of 5 ROIs. For the fifth ROI (i.e.,
a single voxel having MNI coordinates -42 -6 56) I get the following
error:

MarsBaR analysis functions prepended to path
Loaded MarsBaR defaults from base defaults
Design reporting                        :                        ...done
Fetching data                           :                         1/1
Warning: No valid data for roi 1 (points_coordinate_mm_-42_-6_56)
> In maroi.get_marsy at 80
  In m                       ...done
??? Function 'block_rows' is not defined for values of class 'cell'.

Error in ==> marsbar at 976
marsY = block_rows(marsY, row);

Error in ==> spm at 857
evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback.

Could you tell me which is the origin of this problem? And, How can I fix
the problem?

Many thanks in advance.

Federico.

--
Federico Tubaldi, Ph.D Student
Dept. of General Psychology
University of Padova, Via Venezia 8, 35131, Padova, Italy
Present working position:
Visiting student at the Dept. of Neuroradiology
University of Tuebingen, Hoppe-Seyler Strasse 3, D-72076, Tuebingen, Germany
email: federico.tubaldi <at> unipd.it
mobile: 0049 0177 7466815
mobile: 0039 335 1400451

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Manish Dalwani | 25 Aug 19:12

Questions about gray volume through clusters

Dear Marsbar users and Mathew,

I recently learned how to extract mean voxel value (summary time courses) using extract ROI full options on a spm cluster and by exporting it to the matlab workspace.

I have few basic questions. The VBM design I used was in SPM5 using full factorial having 2 groups and 3 covariates. I also used ancova for global normalization. Extract ROI has 2 options 1) obtain raw data 2) From SPM design.

I obtained the raw data first which I assume has not been adjusted for the covariates. When I tried comparing the volumes for the 2 groups using ancova and adjusting for the covariates using SPSS there were no significant differences? Any comment s or suggestions? Maybe I am doing something wrong in SPSS.

If I use the SPM design to get the GM values will it control/adjust for the various design parameters applied including the covariates? Or will it just adjust for global normalization but not for covariates? If I use this option do I have to look for the 'y' or do I still export the summary time course in my matlab workspace to look at the volumes?

Lastly, are the volumes reported in mL?

Kindly advise,
Manish Dalwani
Sr. PRA
University of Colorado

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Jung JeYoung | 7 Aug 13:22

(no subject)

Hello

I'm very new to start using marsbar. I installed it in SPM5 toolbox.
But when I opened it on spm, the window of marsbar didn't appear.
On Matlab, I got the message ;

SPM present working directory:
C:\Program Files\MATLAB\R2006a\work
    ~ - SPM5: marsbar-devel-0.41 toolbox ------------------------------
        Toolbox directory prepended to Matlab path:
        C:\Program Files\MATLAB\R2006a\spm5\toolbox\marsbar-devel-0.41
        ----------------------------------------- 12:01:30 - 07/08/2008

But I didn't get the window.

How can I open it?

Thank you.

Jeyoung Jung

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Mario Aparicio | 4 Aug 12:12

can't read SPM.mat files

Hi,

I try to set a design from file but Marsbar 0.41 does not recognize the SPM.mat file (SPM 5; Matlab 7.4). It seems from the Archive list that some users had the same problem. Has anyone found a solution for this?

Thank you very much

Mario Aparicio
Université Libre de Bruxelles (ULB)

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rkrebs | 31 Jul 20:52

SPM model and marsbar FIR


Dear Matthew and all,

I'm new to this forum and I was wondering if the marsbar FIR time-course
estimation is based on a non-shape assumption even if the original
SPM-design was modeled with a canonical gamma HRF? So in other words, is the
time-course analysis dependent on the modelled HRF or is it a different
disentangeled analysis?

I would be very glad for a short comment!

Best regards,

Ruth
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