[FieldTrip] How to apply ROI mask to grandavg (Sonja Suntrup-Kr?ger)

Sonja Suntrup-Krüger s.suntrup-krueger at uni-muenster.de
Tue Aug 22 09:15:36 CEST 2017

Dear John,
hello everyone,
thank you very much for your valuable response!! Your suggestion is exactly what I had in mind. However, as I see it, if I want to do the multiplication you suggested (multiply the ROI matrix * the pow), the question that remains is how to reshape the ROI-matrix correcly. In other words:

How do the Voxel indices of the linear pos (or pow) -matrix relate to the voxel indices of the dim-cube matrix? I think this is what I need to know to correctly reshape my ROI-matrix from cube (N-ROI X 181 X 217 X 181)  to linear (N-ROI x 7109137) prior to the multiplication step.

Further advice is greatly appreciated!
Thank you very much!


RICHARDS, JOHN schrieb am 2017-08-19:
> Sonja. You are definitely on the right track.

>      pow: [7109137x6 double]  (because there are 6 datasets in the grandavg)
>      pos: [7109137x3 double]
>      dim: [181 217 181]

> The dim are the size of the cube for your source model matrix.  The pow/pos and other matrices are linear.   The linear arrays are a little easier to manipulate, may be the reason that FT decided to use these rather than have 3D matrices.  181*217*181 = 7109137.

> If you create a ROI matrix, it would either be of dimensions, N-ROI X 181 X 217 X 181, or more conveniently you could reshape it into a N-ROI x 7109137.

> Then multiply the ROI matrix * the pow, e.g.,
> [N-ROI X 7109137] * [7109137 X 6] = N-ROI * 6.

> This would sum across each voxel in the source model matrix for each roi.  You can imagine a single ROI of the entire source model (1 x N-dipoles), this would sum across all voxels in the source model.

> Or a single ROI, say of the IFG, in the ROI matrix, would give you the sum of the CDR pow data in the IFG.  Or 10 selected ROIs;  etc etc.

> I also often put the POW data into a MRI volume.  In the MATLAB format a NIFTI MRI volume struct representing this source model would have a img member that is 181 x 217 x 181.  You can simply assign the POW to the img model to get the CDR data into the MRI volume, e.g., MRIVOLUME.img = pow.  Then save or manipulate the MRI volume struct.

> John

> ***********************************************
> John E. Richards
> Carolina Distinguished Professor
> Department of Psychology
> University of South Carolina
> Columbia, SC  29208
> Dept Phone: 803 777 2079
> Fax: 803 777 9558
> Email: richards-john at sc.edu
> HTTP: jerlab.psych.sc.edu
> *************************************************

> -----Original Message-----
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>    1. How to apply ROI mask to grandavg (Sonja Suntrup-Kr?ger)
>    2. Problem with coordinate systems when creating head model
>       (Maria Hakonen)
>    3. bias in cluster stats from density of frequency	sampling?
>       (Nick Ketz)

> ----------------------------------------------------------------------

> Message: 1
> Date: Fri, 18 Aug 2017 12:45:31 +0200 (CEST)
> From: Sonja Suntrup-Kr?ger  <s.suntrup-krueger at uni-muenster.de>
> To: <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] How to apply ROI mask to grandavg
> Message-ID:
> 	<permail-201708181045318218e1ae00002392-s_sunt01 at message-id.uni-muenster.de>

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> Dear all,

> I want to compare task-related brain activation in a ROI  in two groups of subjects. I performed LCMV beamformer analysis on single subject data and, after normalization, created a grandaverage of each group, which I need to compare statistically within a defined ROI.
> Since the option to create a ROI in ft_sourcestatistis is unfortunately no longer available since 2015, I had the following idea to create my ROI:
> By using ft_volumelookup I created a binary mask from an anatomical atlas indicating my ROI in standard space. Now I would like to apply this mask on my grandaverage data. In specific, I want to multiply my mask values (zeros and ones) with the "pow" values in my grandavg.
> This would set all the power values outside my ROI to zero. With the result from this procedure I can then calculate my statistc.

> My binary mask has the dimensions: x,y,z
>      mask [181x217x181 logical]
>      coordsys: 'spm'

> In my grandavg, the dimension "dim" is the same, but the power values ("pow") and their positions ("pos") are listed as a single long  vector for each subject:
>      pow: [7109137x6 double]  (because there are 6 datasets in the grandavg)
>      pos: [7109137x3 double]
>      dim: [181 217 181]
>      coordsys: 'spm'

> My question is: How does the "x,y,z"-data structure of "dim" relate to the "single long vector"-data structure of "pow"/"pos"? If I had this information, I could transform my mask into the same structure and apply it as explained above.

> Your help is greatly appreciated.
> Thank you very much!
> Sonja Suntrup-Kr?ger

> --
> Sonja Suntrup-Krueger, MD
> Assistant Professor of Neurology
> Institute for Biomagnetism and Biosignalanalysis University of Muenster, Germany

> *******************************

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