I am trying to exclude the cerebellum from my seed-to-voxel analysis.  My main question is there a simple way to create a mask like the default mask without the cerebellum in it but that still included white matter sections.

I have done the followed the steps as per a previous post on Conn (https://www.nitrc.org/forum/forum.php?th...) to remove the cerebellum from the analysis...

In image calc in SPM, I input the following options...

input images: conn/utils/surf/mask.volume.brainmask.nii and conn/rois/atlas.nii

expression: 1.*(i2<107)

This works amazingly well.

However, my the original mask (mask.volume.brainmask.nii) contains white matter while my new one doesn\'t.  I have attached images of the default and new mask below.

I reran with the new mask.  I notice two things.

Firstly, my clusters are much more defined.

Secondly, I notice that several of my significant results are no longer significant.

I ran across the following post in which someone asked about why the default mask contains white matter, but no one has gotten back about the question.  Is this likely a reason why many of my clusters do not come through with my cerebellum and white matter free mask?...

\"it seems possible that activations could extend into the WM, and a GM-WM mask might capture this cluster, whereas a GM-only mask might cut off the WM section, preventing it from passing threshold.\"

http://www.nitrc.org/forum/message.php?m...

Is there a simple way to create a version of the default mask which simply removes the cerebellum but still includes white matter?

Thanks again,

Jennifer

I've just edited my above question, just wondering if anyone has any experience with masks?  

Thanks again, 

Jen

Just for future reference, if anyone ever has a similar problem...

I did the following equation in imagcalc

i1.*(i2<107)

This removed the cerebellar GM from the mask.  I then had to go into Brainsuite to manually remove included cerebellar WM and any other parts that looked odd (they have a tool called "mask tool" in which you can alter a mask).  I saved my altered image as a .nii file and opened it in SPM.  This new mask file wasn't binary (all the white parts of the image were large numbers, but the black parts were 0).  Therefore, I just had to change the image into binary in image calc by typing in i1 > 0.  Then I had a updated binary image which excluded GM and WM cerebellum.  

There is probably a much easier way to do this, but this is the long way around the solution.  

Jen