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federico.tubaldi | 20 Sep 22:14
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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.
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KIDLAB | 24 Sep 16:01
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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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KIDLAB | 24 Sep 16:17
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Re: Combining Structural ROIs


Hello again! 

   I just figured it out- the 'or (|)' command actually puts all the voxels
together between them, whereas I don't know what '&' is doing in this case,
because it doesn't work for my structural images.  Using '|' does work.

Thanks!
KIDLAB

KIDLAB wrote:
> 
> 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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Matthew Brett | 24 Sep 19:12
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Re: Combining Structural ROIs

Hi,

>   I just figured it out- the 'or (|)' command actually puts all the voxels
> together between them, whereas I don't know what '&' is doing in this case,
> because it doesn't work for my structural images.  Using '|' does work.

Yes, the '&' does a logical 'and' at each voxel, so retains only
voxels that are present in all three regions.

Best,

Matthew

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Matthew Brett | 24 Sep 19:15
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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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federico.tubaldi | 24 Sep 20:38
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Re: [SPM] SPM5/Marsbar bug

Dear Matthew and dear All,

First many thanks for the link. Now I understand the problem.
By using the code-lines reported on the Marsbar FAQ, I tried to fix it.
However, my programming skills within Matlab and Marsbar are too poor. I
made some unsuccessful attempts.

I would like to try again but I need your help. Specifically, could you
suggest me the code-lines or the specific function/file to be edited in
order to change the linear resampling (i.e., the Marsbar-default
resampling) to the the 'nearest neighbour' resampling?

Best regards,

Federico.

> 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,
>
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jandrews | 1 Oct 18:55
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% 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?
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Gmane