MarsBaR ROI toolbox mailing list ()

jandrews | 1 Oct 18:55

% 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?

(Continue reading)

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stella gialla | 6 Oct 15:26

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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Matthew Brett | 6 Oct 17:40

Re: help error - Cant open image file

Hi,

> 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.

This is quite a common error, it usually happens when the image files
have moved location since you ran SPM for the SPM.mat - see:

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

Best,

Matthew

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Livia King | 9 Oct 02:15

Error when extracting data

Hello,

I am having an error when trying to extract data from an ROI. As soon as I select the ROI for extraction, the program crashes, giving me the following error message

Error in ==> maroi.getdata at 30
if nargin < 2

??? Output argument "vXYZ" (and maybe others) not assigned during call to
"/software/marsbar-0.41/ <at> maroi/getdata.m (getdata)".

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 831
evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback

It seems to be ROI specific -- it reliably happens for certain ROIs, but other ROIs created the same way (by conjuncting two existing ROIs together) work fine. The two ROIs that I created the new ROI from also work fine. If anyone has any thoughts, I'd be grateful! Thanks!

Livia King

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Livia King | 10 Oct 20:38

Re: Error when extracting data

Hello all,
I have a better characterization of the problem I mentioned in my last email (quoted below). It seems that one of the ROIs doesn't work if you try to transform it with the "&" operation. To be more specific, I have two ROIs:

ROI1 - created by selecting an activated cluster
ROI2 - Sphere around a set of coordinates

ROI1 by itself works, as does ROI2 by itself.
ROI1 & ROI2 crashes when I try to extract data
ROI1 & ROI1 crashes as well.
ROI2 & ROI2 works.

Again, this happens only for a couple specific ROIs -- other ROIs made with the same procedure work fine.

Don't know if this helps. Thanks!

Best,
Livia

On Wed, Oct 8, 2008 at 8:15 PM, Livia King <kingl <at> mit.edu> wrote:

Hello,

I am having an error when trying to extract data from an ROI. As soon as I select the ROI for extraction, the program crashes, giving me the following error message

Error in ==> maroi.getdata at 30
if nargin < 2

??? Output argument "vXYZ" (and maybe others) not assigned during call to
"/software/marsbar-0.41/ <at> maroi/getdata.m (getdata)".

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 831
evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback

It seems to be ROI specific -- it reliably happens for certain ROIs, but other ROIs created the same way (by conjuncting two existing ROIs together) work fine. The two ROIs that I created the new ROI from also work fine. If anyone has any thoughts, I'd be grateful! Thanks!

Livia King

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Matthew Brett | 10 Oct 22:03

Re: Error when extracting data

Hi,

> ROI1 by itself works, as does ROI2 by itself.
> ROI1 & ROI2 crashes when I try to extract data
> ROI1 & ROI1 crashes as well.
> ROI2 & ROI2 works.

Have you looked to see if there are any voxels in ROI1 & ROI2?
Presumably there are.  But then, is it possible you have the
resampling problem:

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

Best,

Matthew

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Christian Stoppel | 13 Oct 12:08

How to change pathnames when using batch-mode

Hello marsbar-users,

i’ve a problem using marsbar in batch-mode. Unfortunately my computer crashed and I moved my data to another PC. The bad thing is, that the new volume has a different name (G: instead of D:). Now I am not able to extract marsbar data in batch mode, because all pathnames written in the SPM files refer to the D: Volume… Can anybody explain to me how it is possible to tell marsbar (e.g. the mardo-program) that my files are located at a new volume/path?

Best,

Christian

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Thomas Frodl | 13 Oct 16:35

Re: Welcome to the "Marsbar-users" mailing list

Dear all,

we tried to extract the time series from our fMRI data after filtering with a
design filter as it is possible in the plot menue. Does someone knows how this
is possible? The export only gave us the raw data and not filtered data.

Many thanks

Thomas

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Narumi Katsuyama | 15 Oct 03:52

event duration

Dear marsbar users,

I have questions about "event duration" for extracting the % signal change. 
I have tried to calculate the % signal change in a block design.  When I 
put the block length in second to "event duration" (28 sec), I got extremely 
big values (such as 32.356, 78.416...).  Then I checked the archives and 
found the following comments:

> I'm afraid the % signal change feature should only be used with events
> and not blocks (which are in any case only available with SPM99).  
 (Date: 2005-01-14 22:12:51 GMT)

> For the epoch-based you should enter the duration that corresponds to the 
> onsets you originally specified in the SPM model. 
 (Date: 2006-02-14 02:30:16 GMT)

My questions are:

1. Can I calculate the % signal change in a block design with marsbar?  
2. If I can, which value should I specify for the "event duration"? 

I am using SPM99 for analyses.  Any suggestions are appreciated.  

katz

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Matthew Brett | 17 Oct 19:29

Re: [SPM] Marsbar Error

Hi,

> ??? Undefined function or variable 'mars_blob_menu'.

Is it possible that marsbar is not on your matlab path?  If so, and
you started marsbar when the marsbar directory was your current
directory, and then changed directory (as SPM does when it loads
results), that might explain your error.

By the way, the marsbar list is the best place for marsbar questions -
I've taken the liberty of Cc'ing it there.

Best,

Matthew

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