These
are high resolution (256x256 output) *.MR files. There are generally
2 series: series 2 with ~ 17 images; series 4 with ~124 images.
The latter is used to make 3D volumes. Examples here are for the
tutorial data. To preprocess anatomical images, you'll need several
files from the
Afni
Download page (AnatomyOrig.tar.gz, the Scripts directory, and,
if you don't have it, the rename_anat script from the Recon.tar.gz
package).
Alternatively,
if you'd like a copy of the preprocessed anatomical images, so that
you can work on centering and
aligning
the 3D, then you'll want the files from the
Analysis
area. If you'd like to work with the finished files (3D is already
centered and realigned) then you'll want files from the
Finished
area.
Now
gunzip and untar the AnatomyOrig.tar.gz file. This will create a
new Anatomy subdirectory. (If you aren't working with the tutorial
data, then you should make an Anatomy directory and copy *.MR files
into it.)
>gunzip
AnatomyOrig.tar.gz
>tar
xvf AnatomyOrig.tar
Series
2 Images "2D
Anatomical"
Rename
MR files:
>cd
Anatomy
>rename_anat [at the prompt, enter
the exam and series number, e.g., E21670S2]
Note
that this process will report not being able to find a lot of images.
This is because it is set up to rename 99 images and there are only
17 images in Series 2.
Data
collected after September, 2002?
Check out the new
rename_anat2
or rename_anat3.
Make
a "2D" Structural brick:
Move
up to the parent directory so that the BRIK and HEAD file will be
placed here instead of in the Anatomy directory:
>cd
..
>to3d
-anat -prefix brain Anatomy/E21670S2*
Data
Collected after September, 2002?
A
new header size and new naming strategy necessitate some changes
in protocol. See
Scanner Updates: Header
Size for more details.
Note:
A feature as of late 2001 allows to3d to automatically read the
headers on some anatomy files. In this case, to3d will make the
brik without bringing up the interface. If there is a problem with
the brik or you don't like this (and want to read Bob's poetry),
then you can force to3d to bring up the interface by adding -nosave
to the command, e.g.,
>to3d
-anat -prefix brain -nosave Anatomy/E21670S2*
In
the to3d interface, should you choose or need to bring it up, set
the following:
x
orientation Right to Left
y orientation Anterior to Posterior (if eyeballs are on top)
z orietation Superior to Inferior (if slice 0 is the top
of the brain)
Choose square pixels square, (because x and y dimensions
are the same), slice thickness, z: 6 (this is 5 skip 1),
FOV: 220.
Save
data, quit.
Series
4 (spgr) Images "3D Anatomical"
Use
the series with 100+ images (usually series 4, but sometimes series
3 or 5) to make a 3D volume (E21670S4 will be a series with 124
slices). Don't bother to create a separate subdirectory. Run the
Rename procedure and the to3d procedure as described above. Use
an appropriate prefix, like brain3d:
>cd
Anatomy
>rename_anat
[at the prompt, enter the exam and series number, e.g., E21670S4]
>to3d
-anat -prefix brain3d seqplus Anatomy/E21670S4*
to3d
is the command. -anat is a flag telling afni that this is
an anatomical file. -prefix is a flag that is followed with
the prefix that you want to be assigned to the output file. seqplus="sequential
in the plus direction". Finally, list the path to the files
to be used in the BRIK.
In
the
to3d window, make the following settings (and keep careful notes,
it is very confusing):
Choose
square pixels, slice thickness, z: 1.5 (use square
or irregular radio buttons to set). Field of view: 250
Assume a sagittal view, set
x orientation: Anterior to Posterior
y orientation: Superior to Inferior
z orientation: Left to Right
Centering
If
you'd like a copy of the preprocessed anatomical images, so that
you can work on centering and aligning the 3D image, then you'll
want the files from the
Analysis
area.You should have a set of values somewhere on a scansheet that
will help you to set the center points (However, see also "Aligning
Series 2 and Series 4 Images" below). For the tutorial:
A 4.0, I 0.2, L 4.2.
"A" corresponds to Anterior (slices begin anteriorly)
and 4 should be added to the x origin to compensate for the location
of the patient's center relative to the k-space center.
"I" corresponds to Inferior (slices end inferiorly) and
0.2 should be subtracted from the y dimension, etc. In the gui interface,
you must click each yellow button next to the dimensions in the
upper right corner, so that you can set the values (do NOT reclick
them when you are done, as this sets them back to their default
values). So, in our tutorial:
X: 124.5117+4.0=128.5117
Y: 124.5117-0.2=124.3117
Z: 92.25+4.2=96.45
Save
Data, Quit.
Aligning
the 3D Image
Unfortunately,
when you display functional images overlaid on the 3D (Series 4)
anatomy, they (the functionals) are likely to be noticeably off
in terms of location on the anatomy. This is typical, and indicates
that you must go beyond the centering (described above) and align
the image manually to improve the overlay for Series 4. Keep in
mind that here at the U of A, Series 2 (the 2D) is taken in the
same plane as the functionals, and overlays of the functionals on
the 2D are correct. We must, therefore, move the center of the Series
4 (3D) image to line up with the 2D image.
Open
both images (the 2D and the 3D) in Afni (use the "new"
button in the lower left corner to get a 2nd set of Afni windows).
Display
activations (Define Function. This brings up additional widgets,
a correlation bar and color bar. Select 4 colors, change orange
to red and "set" the color change. If you leave the correlation
slider at r=.5000, you'll rarely see activation, so check to make
sure you have lowered it to 0. Click "See Function". You
probably want to display a functional analysis with some reasonable
p-value, which assumes you have done the analysis and have some
reasonable file to display. Check under "Switch Function").
Find
a distinct point that you can see on both images. The most superior
point of the infundibular stalk (that little white dot that shows
up on axial slices, just posterior to the optic chiasm; see the
crosshairs in the image below) is a good choice. Start with the
Series 2 image (the 2D image, brain+orig.BRIK) because it will have
fewer slices, and so you are more likely to be able to find the
same point in the 3D, than vice versa):
Put
the crosshairs on the point and note the coordinates in the upper
left corner of the afni window (e.g., -0.430 R, -24.492 A, -36.000
I; these values come from the tutorial data set):
Now,
in the 3D image, try to find the same anatomical landmark in a slice
that is as similar to the 2D slice as you can manage. Consider the
image below. The infundibular stalk is visible, though this is not
the most superior point of the stalk in the 3D. Approximately equivalent
amounts of the cerebellum show in both images. The lateral ventricles
are not showing on either image. Look carefully at detailed anatomical
features in the 3D slices near your landmark and choose your final
slice based on the totality of shared features.
Keep in mind that this is an art, and that your match will only
be close, not exact.
In
some cases, you may need to use 3drotate to rotate one image to
be closer to the other (but you should not need to do this for the
tutorial). Once you have found the same anatomical landmark on the
most similar slice possible, note the coordinates (again, these
values are from the tutorial set): 6.45 L,
-24.996 A, -29.985 I.
Calculate
the differences between the location of the anatomical landmark
in the 2D and 3D images:
2D |
3D |
Difference |
-0.430
R |
6.45
L |
6.88 |
-24.492
A |
-24.996
A |
0.504 |
-36.000
I |
-29.985
I |
6.015 |
Now
determine the direction in which you'd have to move the center point
of the 3D image to align it with the 2D image. For our tutorial
image, we need to make the following changes: 6.88 R, 0.504 P,
6.015 I. This should be relatively straightforward from an examination
of the landmark coordinates for the two images and the differences
between them.
Finally,
make appropriate additions and subtractions from the current center
points (see Centering above)
For
the tutorial data:
X: (A-P) 128.5117-0.504=128.0077
Y: (S-I) 124.3117-6.015=118.2967
Z: (L-R) 96.45-6.88=89.57
To
make the actual changes as calculated, use 3drefit. Here is the
command you'll want to enter for the tutorial data:
>3drefit
-xorigin 128.0077 -yorigin 118.2967 -zorigin 89.57 brain3d+orig.BRIK
Sometimes
this takes a few tries to get it right. You should end up being
able to move the crosshairs around on the two images and get similar
xyz coordinates.
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