How can I check the slice number for axial, coronal and sagittal views correctly with mrview?
I am using mrview to visualize track density (TDI) output. But my object of interest seems to be present in different slices, everytime I run the algorithm for TDI.
Can some one shed some information on this.
I don’t know if that’s visible with
mrview, but you can use the
mrinfo command on the image, which will give you the dimensions (i.e. slice number) in axial, coronal and sagittal view (and number of volumes as 4th dimension, if it’s a 4D image)
I’m not sure what you mean here. The slice number is displayed on the bottom left, in the line that starts with
voxel:. This indicates the coordinates of the voxel currently under the crosshairs, indexed from zero. In axial view, the 3rd entry is the slice number (the z coordinate); in sagittal, the first number (the x coordinate), and in coronal view it’s the second entry (the y coordinate). Any numbers after the first three indicate the volume number, etc, depending on the dimensionality of the image.
What I’m struggling to understand is what the issue is with your TDI application. What is your object of interest? And when you run the algorithm for TDI, what commands are you using? One possibility (depending on exactly what you mean) might be that if you run
tckmap without the
-template option, the field of view of the image is determined from the input streamlines, so that might introduce variability into the exact positions of the bounds of the image. But that should still give you the same output for the same tractogram, so this would only be a problem if you regenerate the tracks as well.
Does this answer your question…?
Yes, the second half of you reply answers my question.
I was looking at the thalamic nuclei and using TDI for that purpose.
I was generating a new tractogram everytime, by changing parameters such as the cutoff, seed points and length of tracks.
As per you suggestion, the image is being determined from the input streamlines.
Is this one of the reasons causing me to see the same nuclei in a slightly different slice (one or two slices backward or forward in coronal or sagittal view)?
Can I resolve this by using the template option?
But does that mean I have to register my images to the template or MNI space?
Ok, glad I guessed that right. To answer your other question: no need for registration, all the template image does is provide the field of view and voxel size, so the output image will match that. If you want, you can use one of your existing TDI as the template for the subsequent ones, for instance, and that way they’ll be guaranteed to match.