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I am new to fMRI field. In many fMRI studies like This Study a voxel wise comparison is made across subjects and controls . As we know that dataset in fMRI in the form of 3D matrix like Subjects x TimePoints x Voxels that is on each person we have bunch of time points and on each time points we have voxel values as voxel is unit of measurement in bold signal in the brain that is brain is divided into small cubicle voxels.

My specific question No.1 is that if we have a dataset consisting of 20 control and 15 subjects with 5000 voxels and 200 time points on all persons then we will have two 3D matrices in following form

For Subjects: 15 x 200 x 5000

For controls: 20 x 200 x 5000

Now how voxel wise comparison would be made between two subjects as these datasets are not balanced in persons or first dimension.

My specific question No.2 is that how regions are compared between those two group like this has been done on page 2(13).

My Understanding

For question No.1 my understanding is that a single matrix is made for each group by reducing the person(subject/control) dimension that is we will have two 200 x500 matrices average over individuals in each matrix and then the voxel wise comparison will be made using t test in any two voxel as each voxel will have 200 time points.

For question No.2 my understanding is that for a typical brain area like "Right thalamus" A group of voxel called cluster like 147 as used in the paper is organized and then voxel vectors are formed for both groups averaged over individuals like out of 147 voxel vector a typical voxel vector will have 200 values and that will be compared.

lastly some times the volumes are reported in the specific brain region like "Right thalamus" in cc and again my question is that how theses volumes are computed?

So I am totally messed up here and need guidance here in my understanding ?

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    $\begingroup$ Welcome. Nice stuff. Please try to avoid asking multiple questions in one post. If they are sufficiently unrelated I would encourage you to split this post up in its three respective questions. That greatly increases the chance of receiving answers. $\endgroup$ – AliceD Apr 23 '18 at 20:08

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