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Create Tables of Cluster Overlap With Brodmann Area and Anatomic Area

Page history last edited by PBworks 13 years, 6 months ago

The WFU_PickAtlas SPM toolbox comes with a Brodmann Area atlas and an anatomical atlas in MNI space. I have written a script that finds the overlap between a Cluster Mask and either of these MNI atlases and reports the percent overlap. This can be used as a rough guide for localization. Of course, there are caveats about how reliable this method is; for example, spatial normalization is not perfect, and it's possible that the atlases have errors. So, use this approach at your own risk!

 

(1) Start a 16-bit integer Cluster Mask, such as the one written out to disk in step 12 of Cluster Detection. For the sake of illustration, let's assume that the Cluster Mask is named Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.img. Of course, your own Cluster Mask will probably have a different name.

 

(2) Log onto the machine named medx, and get into a tcsh shell. For Brodmann area overlap, run the command

 

estimateBaOrAnat.csh Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.img B

 

This will generate a text file named Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.BA.txt.

 

(4) For anatomical area overlap, change the B at the end of the command to an A, e.g.

 

estimateBaOrAnat.csh Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.img A

 

This will generate a text file named Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.Anatomical.txt.

 

(5) Open up the text file, perhaps in gedit. Or run the command

 

cat Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.BA.txt

 

or

 

more Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.BA.txt

 

 

You might see an entry like the following:

 

==================================

Cluster #6

Total number of voxels in the overlap = 79

Area Number of Voxels Percent of Total Number of Voxels Left-Right Laterality

Sub-Gyral 51 64.557

Superior Frontal Gyrus 9 11.3924

Middle Frontal Gyrus 9 11.3924

Anterior Cingulate 10 12.6582

==================================

 

If you load this Cluster Mask into MEDx and perform pixel sampling (see section 4.5 in Chapter 4 of the MEDx User's Guide), you'll find voxels that are set to a value of 6. These voxels constitute Cluster #6.

 

The above output indicates that Cluster #6 had 79 voxels that overlapped with voxels defined in the anatomical atlas. If you run the following command

 

countVoxelsInCluster Cluster.Zmap.Dyslexics-Controls._2.33._3.1.60.26.0.img 6

 

the program returns 79, indicating that this cluster contains 79 voxels. Therefore, all 79 voxels in this cluster overlapped with voxels defined in the anatomical atlas. It is possible for some voxels in a cluster to fall outside of defined areas in the atlas, though.

 

The list below indicates that 51 voxels were in an area defined as Sub-gyral (i.e., white matter) in the atlas; this is 64.557% of 79. But 9 voxels were in Superior Frontal Gyrus, 9 in Middle Frontal Gyrus, and 10 in Anterior Cingulate, as defined by the atlas.

 

(6) Laterality is always a tricky issue. You must know ahead of time which unimanual left hand finger tapping. If you feel comfortable relying on the DICOM transfer and MEDx handling laterality properly, you can perform a DICOM transfer, note which sides MEDx "thinks" are left and right, analyze the data, and see where activations fall in "left" and "right".

 

That said, let's suppose that you know that Cluster #4 is on the left side and Cluster #5 is on the right side. Then, you might see output such as the following:

 

==================================

Cluster #4

Total number of voxels in the overlap = 91

Area Number of Voxels Percent of Total Number of Voxels Left-Right Laterality

Sub-Gyral 45 49.4505 OppositeLaterality

Inferior Frontal Gyrus 40 43.956 OppositeLaterality

Middle Frontal Gyrus 6 6.59341 OppositeLaterality

==================================

Cluster #5

Total number of voxels in the overlap = 19

Area Number of Voxels Percent of Total Number of Voxels Left-Right Laterality

Middle Temporal Gyrus 3 15.7895

Superior Temporal Gyrus 16 84.2105

==================================

 

Note that the words "OppositeLaterality" appear in the lines for Cluster #4, whereas they don't for Cluster #5. This indicates that Cluster #4 is on the opposite side from Cluster #5, whatever that is. You need to know ahead of time which side is left and right; this program provides the words OppositeLaterality only as a convenience. This program is not smart enough to figure that out for you! Once you figure out which side is which, you can use the presence or absence of the words OppositeLaterality in this text output file to indicate laterality.

 

(The ANALYZE format header does not encode enough information to fully describe orientation. The new NIfTI format does, but unfortunately MEDx doesn't recognize NIfTI format.)

 

It is possible for clusters to span the midline, and to therefore have some voxels that are on the left and some that are on the right. For example, in the breakdown for Cluster #1 shown below, there are two lines with and two lines without the words OppositeLaterality, indicating that some of the voxels were on the left and some were on the right.

 

==================================

Cluster #1

Total number of voxels in the overlap = 149

Area Number of Voxels Percent of Total Number of Voxels Left-Right Laterality

Extra-Nuclear 11 7.38255

Thalamus 122 81.8792

Extra-Nuclear 2 1.34228 OppositeLaterality

Thalamus 14 9.39597 OppositeLaterality

==================================

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