Generating statistical maps with FDR correction

Hi Matthew,
    I've been using a modification of your batch script run_tutorial.m 
in order to define ROIs by combining my statistical maps with Marsbar's 
structural ROIs (using an '&' operation).  So far it's been working 
without a hitch.  Thank you for making this script publically available; 
I find it exceedingly useful.

    As you know, your script generates statistical maps with 
*uncorrected* p values.  Could you please tell me how to generate the 
statistical maps with FDR correction (say an FDR of 0.05)?  I tried to 
do this by using spm_P_FDR.m, but it seems so complicated. I haven't 
been able to get it to work so far.  So I figured maybe you know of a 
simpler way of correcting for FDR.

    Thank you very much and best regards,
    Jay Hegdé
    U Minnesota
    Minneapolis, MN, USA
    hegde <at> umn.edu

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error while extracting raw timeseries

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functions called by build and transform buttons

Dear Friends:

I'm trying to create VOIs using the buttons of "build" and "transform" for
individual subjects.  I'm wondering if any one can tell me the corresponding
functions are called by these buttons.

Best Regards

Jiansong 

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binary mask

Dear friends,

I have a image file which I got from a conjunction analysis. I want to use this
image combined with whatever I'm interested in AAL then to define a spheric ROI.
First I want to make a binary mask for this conjunction image. I use Marbar-
build-image(selecting the conjunction image)
--keep binary--yes
--apply function? Here I don't know I should select yes or no. I have
thresholded the conjunction image as p<0.005. If selecting "no", does it mean
the binary is either or p>0.005? If selecting "yes", what function should I
apply then still keep p<0.005? Could anybody help me out? Thanks!

Best,

Chunhong

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PET data-covariate and scaling from SPM design

Dear marsbar user,

I m a very new marsbar user but convince that marsbar would give me large
opportunity to progress in my work. I am working on parametric PET data in
differents groups of analysis that represents in each voxel the absolute
values of transporter availability. There is an important known effect of
age on the PET signal in some brain regions that I had controlled in SPM
analysis with age as covariate in SPM5. I would like to extract signal in
cluster with marsbar that already removed the efffect of age on the signal
in order to search for other correlations that could potentialy be
influenzed by age. My question is : When I extract data from my cluster of
interest with full options. Must I select spm design and scaling from spm
design (and not raw data) in order to obtained no realistic values of
transporter but rescaled values corrected for the influence of age in the
signal ? 
Sorry for my very naive question and Hope somebody could help me. 

Best regards,
Claire

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Re: binary mask

Hi,

> I have a image file which I got from a conjunction analysis. I want to use this
> image combined with whatever I'm interested in AAL then to define a spheric ROI.
> First I want to make a binary mask for this conjunction image. I use Marbar-
> build-image(selecting the conjunction image)
> --keep binary--yes
> --apply function? Here I don't know I should select yes or no. I have
> thresholded the conjunction image as p<0.005. If selecting "no", does it mean
> the binary is either or p>0.005? If selecting "yes", what function should I
> apply then still keep p<0.005? Could anybody help me out? Thanks!

Try the function:

i1 ~= 0

if you just want all non-zero voxels to be within the ROI...

Best,

Matthew

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Re: functions called by build and transform buttons

Hi,

> I'm trying to create VOIs using the buttons of "build" and "transform" for
> individual subjects.  I'm wondering if any one can tell me the corresponding
> functions are called by these buttons.

Have a look at marsbar.m.  If you search for 'build', you'll find
around line 475, that the build function calls mars_build_rois.  The
transform function calls one of:

marsbar('combinerois') (marsbar.m line 588)
marsbar('fliplr') (marsbar.m line 630),

Best,

Matthew

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Creating ROIs using getdata() vs '&'

Hi,
     I like using both getdata () and the & operation for creating ROIs,
depending on the output I want.  But I'm having trouble understanding how
they work -- specifically, why they produce different ROIs in the following
case:

     I have a binarized ROI ('myroi') of type maroi_matrix.  I have a T
contrast image 'spmT_0001.img'.
I read in the contrast image and convert it to an maroi_matrix object,
'act_roi'.  The 'spmT_0001.img' and 'act_roi are otherwise identical;
neither is binarized.

        newroi1 = myroi & act_roi;
        newroi2 = getdata(myroi, spmT_0001.img);

     I expect newroi1 and newroi2 to be identical, but they're not.  Why is
this?
     Thank you very much,
     Jay
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Re: Creating ROIs using getdata() vs '&'

Just so there is no misunderstanding about how I created an ROI using
getdata(), I wish to add that to create rois using getdata(), I used the
vXYZ output of getdata() and converted into real coordinates.
Thanks,
Jay

jayhegde wrote:
> 
> Hi,
>      I like using both getdata () and the & operation for creating ROIs,
> depending on the output I want.  But I'm having trouble understanding how
> they work -- specifically, why they produce different ROIs in the
> following case:
>      
>      I have a binarized ROI ('myroi') of type maroi_matrix.  I have a T
> contrast image 'spmT_0001.img'.
> I read in the contrast image and convert it to an maroi_matrix object,
> 'act_roi'.  The 'spmT_0001.img' and 'act_roi are otherwise identical;
> neither is binarized.
> 
>         newroi1 = myroi & act_roi;
>         newroi2 = getdata(myroi, spmT_0001.img);
> 
>      I expect newroi1 and newroi2 to be identical, but they're not.  Why
> is this?
>      Thank you very much,
>      Jay
> 

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SPM5 and MarsBaR 0.41, problems with drawing ROI

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