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Combining Seeds

Hello All,

I am wanting to conduct some ROI-ROI, and seed-voxel analysis using the default ROI's within the CONN toolbox. I am a bit confused about how to combine multiple ROI's or to use an entire network (as defined in CONN17a) as a single seed to use during first/second level analysis. Thanks for any guidance.

From,

Humza Ahmed

RE: Combining Seeds

Hi Humza,

Unless I understood your question incorrectly, you could just add different ROI mask files together to create one single ROI file. You can read them into MATLAB and do it, or just use 'imcalc' utility of SPM to read all masks together, and add them.

If you are referring to atlas files with different intensities for different ROI and you just want to select a sub-set of these ROIs you could do the following:

vol = spm_read('atlas.nii'); % The atlas file which you want to read from

vol_data = spm_read_vols(vol);

intensities = [10 20 30]; % The intensities which you want to convert to ROI

dummy_mat = zeros(size(vol_data);

for i = 1:length(intensities)

tmp = vol_data==intensities(i);

dummy_mat = dummy_mat + tmp;

end

vol.fname = 'modified_atlas.nii'; % The name of the new nifti file which you want to write

spm_write_vol(vol, dummy_mat);

In case of probabilistic atlases, you would want to introduce an additional thresholding line above.

Hope the above helps.

Best
Pravesh

Originally posted by Humza Ahmed:

RE: Combining Seeds

Thanks I would like to use a subset of ROI's within CONN's default atlas.nii file as you had mentioned. How would I determine which intensities refer to the Regions I am interested in. For example how would I get the intensities used to label the PC (Cingulate Gyrus, posterior division)?

RE: Combining Seeds

Hello again,

In your "rois" folder in the Conn installation directory, you will see a file named "atlas.txt' (not the .info file). You can find all names corresponding to intensities (serial fashion). I have an older version of Conn installed (15h) where line number 56 is PC (Cingulate Gyrus, posterior division). So, intensity 56 should correspond to that division. I have not checked in newer version of Conn (in case then atlas has been updated).

Best
Pravesh

RE: Combining Seeds

Dear Humza and Pravesh,

I am interested in this too. I would like to create a limbic system network made up of a few core seeds (i.e., amygdalae, ACC, accumbens, hippocampus etc) and use this network as a single seed/source for seed-to-voxel analysis. Is it as simple as simply holding down Ctrl and select all the seeds I want, then select "average" in the "between-sources contrast" and then click "results explorer"; or do I need to go through some additional steps?

Thank you!

Marie

RE: Combining Seeds

Hi Marie,

Yes setting the between-sources contrast and looking through the results would be enough.

In general the between sources contrast is defining how to weight the first level parameter estimates across the different sources. If you wanted an average of 2 rois you would then want to weight them equally by specifying a weight of 0.5 and 0.5. Similarly you could specify unequal weights if desired.

The approach Pravesh provided in matlab is useful if wanting to use a particular roi for analysis or visualization outside of conn.
Originally posted by mscahart:

RE: Combining Seeds

Hi Humza,

Thank you so much for your prompt reply!
What is the best way of choosing if a weight of 0.5 and 0.5 would be appropriate, or if unequal weights would be better? If we take the example of the Salience network provided in the toolbox, how would I know which weights to apply?

Marie