Back to PLS Helpcluster report coordinates
Posted on 06/10/10 19:12:52
Number of posts: 4
Hi,
the MNI coordinates indicated in the cluster report seem to be off. For example, one peak coordinate (in mm) is 8, -67.7, 3.7. When using the XYZ(mm) window in PLS, the location is identified somewhere in the cerebellum. However, when locating this coordinate on the mni brain in SPM, it is close to the cuneus. Transformed into talairach space,the programm talairach daemon labels this spot as cuneus as well.
Any advice on what may cause the discrepancies?
Thank you,
Michael
Replies:
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Posted on 06/11/10 04:40:35
Number of posts: 394
quote:
Hi, the MNI coordinates indicated in the cluster report seem to be off. For example, one peak coordinate (in mm) is 8, -67.7, 3.7. When using the XYZ(mm) window in PLS, the location is identified somewhere in the cerebellum. However, when locating this coordinate on the mni brain in SPM, it is close to the cuneus. Transformed into talairach space,the programm talairach daemon labels this spot as cuneus as well. Any advice on what may cause the discrepancies? Thank you, Michael
The coordinates posted in the cluster report are based on the information provided in the image header for your data. They are computed from the specified image origin (usually the anterior commissure) and the distance of a given point from the origin calculated in matrix coordinates (XYZ) and mm's (XYZmm) using the voxel dimensions that are in the image header. The anatomical label of the coordinate is independent of this and depends on the template you use to transform your data. Hi, the MNI coordinates indicated in the cluster report seem to be off. For example, one peak coordinate (in mm) is 8, -67.7, 3.7. When using the XYZ(mm) window in PLS, the location is identified somewhere in the cerebellum. However, when locating this coordinate on the mni brain in SPM, it is close to the cuneus. Transformed into talairach space,the programm talairach daemon labels this spot as cuneus as well. Any advice on what may cause the discrepancies? Thank you, Michael
The specific location you indicate is in a tricky part of the brain as its the transition between cerebellum and occipital cortex. My advice is to take a close look at the coordinate in space of the functional images you used for the analysis to see where it lies. The anatomical labels provided by other software are approximations and should not be taken as ground truth without looking at the location in your specific data set.
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I'm Online
Posted on 06/11/10 11:51:26
Number of posts: 291
It might be caused by the size of the voxel. This is especially true when you have large voxel size and the transition area is quite sensitive. The reason is that the peak location in mm is converted from the peak location of voxel, which is the minimum unit in our calculation.
In SPM, the display is even interpolated into more detail resolution. When you zoom in (click Tool, then click Zoom in), you will know what I mean. Basically, you can have many more detail location within a voxel. Those location may even have different intensity value.
The best way to clarify this issue is to test an image with landmarks. I just did the test, and here's the result:
Suggestions:
In SPM, the display is even interpolated into more detail resolution. When you zoom in (click Tool, then click Zoom in), you will know what I mean. Basically, you can have many more detail location within a voxel. Those location may even have different intensity value.
The best way to clarify this issue is to test an image with landmarks. I just did the test, and here's the result:
- Take "avg152T1_LR_nifti.nii" from: http://nifti.nimh.nih.gov/nifti-1/data
- Display it with SPM5
- Focus on the cornor of "R", which is in upper right area of the axial view
- The cornor of letter "R" is located from [50.5 12.5 0] to [51.5 13.5 0]
- View it with pure voxel based program: nii=load_nii('avg152T1_LR_nifti.nii');view_nii(nii);
- You will find that the corner should be either [50 12 0] (inside) or [52 14 0] (outside). This is correct since the voxel size is 2mm in "avg152T1_LR_nifti.nii" image.
Suggestions:
- Using image with more resolution (smaller voxel_size). However, this might bring "out of memory" problem.
- Using image with more resolution, plus a pre-defined brain region (a binary image, only true in the area that you would like to analyze, any voxel outside of this area will be treated as non-brain area, and will not be considered to analyze). However, the result might be different from the one that you run analysis with whole brain area.
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