Re: [Marsbar-users] Warning: No valid data for roi

[Joe S. <dur...@gm...>]

Dear Matthew

Thanks for your reply. I already tried the link you provided me, my
analysis
now works for some ROIs, but not for all. I had a look at the fMRI-data
(both
native images and after pre-processing), the ROIs which are still not
working
do not appear to be at the edge of the brain....
Could there be any other reason for this error, or am I simply missing
something?

Best,
Joe

Matthew Brett <matthew.brett <at> gmail.com> writes:

>
> Hi,
>
> Sorry to be slow to reply, you caught me in Cuba without much email
access.
>
> On Wed, Aug 1, 2012 at 7:10 AM, Joe Simon <durdantyler <at> gmx.net>
wrote:
> > Dear marsbar-experts
> >
> > I want to extract raw ROI-data from a 2nd-level analysis.
> > I start by loading my SPM.mat file ("Set design from file"), when I
want to
> > "extract ROI data" I get the following message:
> >
> > MarsBaR analysis functions prepended to path
> > Design reporting
   :                        ...done
> > Fetching data                           :                         1/1
> > Warning: No valid data for roi 1 (sphere_3-9_3_-8)
> >> In maroi.get_marsy at 80
> >   In marsbar at 989
> >   In         ..e
> >
> > I tried to identifiy the problem by using batch mode:
> >> marsbar('on')
> >> D = mardo('SPM.mat');
> >> R = maroi('sphere_3-9_3_-8_roi.mat');
> >> Y  = get_marsy(R, D, 'mean');
> >
> > I get the following message:
> > Warning: No valid data for roi 1 (sphere_3-9_3_-8)
> >> In maroi.get_marsy at 80
> >
> > N.B.: marsbar seems to set the modality of my design as "pet", I wasn't
able
> > to change this
> >
> > I further explored the data:
> >> Y = images(D)
> >>> data = getdata(R, Y, 'nl')
> >
> > data =
> >
> >    -0.9607   -0.9427   -1.1762   -0.7643   -0.2506
> >     0.0021    0.5151    0.2069    0.2852    1.1370
> >    -0.3894   -0.3788    0.0704    0.1754    0.3875
> >    -0.1195    0.2622   -0.7753   -1.1122   -0.9496
> >     0.2035   -0.0060   -0.2449   -0.0924   -0.3101
> >     1.2057    1.0827    1.2792    1.6498    1.6132
> >     1.0395    2.0230    1.2155    0.0573    1.8966
> >     0.1499    0.6682    0.8490    0.7970    1.5199
> >     1.1097    0.1878    0.8706    1.8961    1.0043
> >    -0.0594    0.3875    0.1746    0.0395    0.3753
> >     0.6346    0.9271    0.5784    0.5276    0.1759
> >        NaN       NaN       NaN       NaN       NaN
> >     1.7645    2.2654    2.6787    2.4486    3.4638
> >     0.9348    1.9641    1.8862    1.6229    2.9834
> >     0.4289    0.6866    0.1763   -0.2493    0.1948
> >     1.3276    2.2344    2.0987    1.5240    2.7520
> >     1.5423    1.8862    1.7336    0.9675    1.5139
> >     0.9408    1.7385    1.8812    2.4381    2.2321
> >    -2.0215   -0.7024   -1.1765   -1.1612    0.2732
> >
> > The "NaN" column corresponds to one specific subject, I presume this is
the
> > reason it doesnt work? I checked the subject in question, the data
seems to
> > fine...
>
> I guess for that subject the ROI was close to the edge of the brain?
> Did you see
http://marsbar.sourceforge.net/faq.html#why-do-i-get-a-no-valid-data-for-roi-warning-when-extracting-data
> ?  Does that fix work for you?
>
> Best,
>
> Matthew
>
>
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