,
to bring up the landmark window:Cropping means setting two landmarks that define the extents of the data that NVM will load. This is a good thing to do because it preserves screen space and makes NVM faster since it only has to deal with useful data. The two landmarks are: "MIN_CROP" and "MAX_CROP". See the scan coordinate system, and note that:
MIN_CROP = minimum cropping landmark = right - superior - posterior corner of the data, and
MAX_CROP = maximum cropping landmark = left - inferior - anterior corner of the data.
The following assumes that you have loaded cronally acquired scan.
Click on the Landmark Tool, ,
to bring up the landmark window:
The text (e.g. "Right -> Left") in this window will help you remember where the minimum and maximum cropping landmarks are located: minimum is the first column (right, superior, posterior), and the maximum is the next.
In the Landmark window, choose "MIN_CROP" from the drop-down menu called "Choose a Landmark:". If you have already set this landmark, NVM will jump to that location and display the landmark in all views and display the coordinates for this landmark. If not, the coordinates shown in the window will be "-1".
Select the arrow tool, 
,
and adjust the slices in each view so that the projection lines cross at the
minimum cropping point. To do this, first double-click on the sagittal image
near the upper right corner (this is the superior posterior side of the subject)
so that the projection lines pass through the extent of the brain that you
want to keep. This will adjust the slices displayed in the coronal and axial
views. Now click on the scroll bars of the coronal and axial views to fine-tune
the area of the scan that will be kept. Click on the arrows in the coronal
view so that you find the coronal slice where the brain is present in one
slice and not in the next (or, you can use the skull boundary if you want looser
cropping). Leave that slice showing and do the same for the axial view. You
might have to adjust the brightness and contrast so that you can see the brain.
The coronal view will set the posterior extent of the scan that will be loaded
and the axial view will set the superior extent.
Now click on the sagittal image scroll bar to determine the rightmost extent. You can watch the projection lines in the coronal view to make sure the MIN_CROP landmark is set at the subject's right side – note that this is on the left side of the screen since MRI images are acquired as if you are looking at the subject's face. Again, find the sagittal location where the brain is present in one slice and not the next, and leave the non-brain slice showing.
With the three views set at the right-superior-posterior slices of the brain,
the minimum cropping landmark is where the projection lines cross in all of
the views. To set the landmark, click on the landmark tool, ,
again. The "MIN_CROP" landmark should still be selected. Now click on any view
where the projection lines cross. This sets the landmark location. You can
fine-tune the location by clicking on the arrow buttons.
In the Landmark window, choose "MAX_CROP" from the drop-down menu. The following procedure is similar to that for setting "MIN_CROP" except that you will be locating the Left-Inferior-Anterior-most slices of the brain.
Select the arrow tool, ,
and set the sagittal slice so you can see the brain again by clicking in the
middle of the scroll bar. Then double-click on the sagittal image
towards the lower left (the anterior inferior side of the
subject) so that the projection lines pass through the extent of the
brain that you want to keep. This will adjust the slices displayed in the coronal
and axial views. Next, click on the scroll bars of the coronal and axial views
to fine-tune the area of the scan that will be kept. Again, adjust
the views so that you find the location where the brain is present
in one slice and not in the next. The coronal view will set the anterior extent
and the axial view will set the inferior extent of the scan that will be loaded.
You might want to change to a sagittal slice that will show the location of
the bottom of the cerebellum or you might choose a slice that shows the brain
stem.
Now click on the sagittal image scroll bar to determine the leftmost extent. You can watch the projection lines in the coronal view to make sure the MAX_CROP landmark is set at the subject's left side – note again that this is on the right side of the screen. Find the sagittal location where the brain is present in one slice and not the next, and leave the non-brain slice showing.
With the three views set at the left-inferior-anterior slices of the brain,
the maximum cropping landmark is where the projection lines cross in all of
the views. To set the landmark, click on the landmark tool, ,
again. The "MAX_CROP" landmark should still be selected. Now click
on any view where the projection lines cross to set the landmark location
and then fine-tune by clicking on the arrow buttons.
You must save the landmarks that you just set. In the File menu of the Landmark window (not the main NVM window), choose "Save". The next time you run NVM and load this scan these cropping landmarks will be used so that only the part of the scan that you have specified will be loaded.