Jim has six tools to help you get the best out of your images.
Note: if you want to reverse the order of the slices,
specify a step of -1, with the first slice equal to the number of
slices in the image, and the last slice as 1.
You can also specify extraction of all except the slices in the
list by selecting
When you have set up the slices you want to extract, select the
Input Image by clicking on the icon,
or by typing in the folder (directory) and file name of the image, or by pressing the right mouse
button and selecting from the menu of recently-used images.
The Slice Extractor Tool
Selecting Slice Extractor
from the Organise
menu
of the main display
frame brings up the Slice Extractor Tool:
The Slice Extractor tool takes a single input image, extracts some
of its slice, and uses those extracted slices to create a new image. The new image will be of
the same type as the input image, but with fewer slices. The
new image can either be saved to disk, or loaded into Jim
depending on your selection:
There are several options for your choice of slices to extract:
The Image Concatenator Tool
Selecting Image Concatenator
from the Organise
menu
of the main display
frame brings up the Image Concatenator Tool:
The Image Concatenator tool takes multiple input images and pastes
all the slices from all the input images end-to-end, in order, to
form a new image. The new image will be of
the same type as the first input image. The
new image can either be saved to disk, or loaded into Jim
depending on your selection:
First, select the images to be concatenated by clicking on the
on the button. This will bring up a
File Chooser from which you can select
one or more input images. To select more than one image file, press the
"Control" key down while making your selection. To select all files
in a list, select one file at the top of the list, press the
"Shift" key down, and select a file at the bottom of the list.
You can select any files from the list in this way.
You can add further images to the list of images to be concatenated by clicking on the button at any time.
Ensure that the images are in the order in which you want them to be concatenated. If they are not in the right order, select one or more images in the displayed list to move, and the click either the button or button to get them in the right order.
You can remove all the images from the list by clicking the button, or remove just some of the images by first selecting them, and then clicking the button.
Now click on the button to do the
concatenation. If you have chosen to save the result to disk, then a
File Chooser will pop up, prompting
you to choose a file name for the new image. Otherwise, the result
will be loaded into Jim.
First, select the images to be interleaved by clicking on the
on the button. This will bring up a
File Chooser from which you can select
one or more input images. To select more than one image file, press the
"Control" key down while making your selection. To select all files
in a list, select one file at the top of the list, press the
"Shift" key down, and select a file at the bottom of the list.
You can select any files from the list in this way.
You can add further images to the list of images to be interleaved by
clicking on the button at any time.
Ensure that the images are in the order in which you want them to be
interleaved. If they are not in the right order, select one or more
images in the displayed list to move, and the click either the button or button to get them in the right order.
You can remove all the images from the list by clicking the button, or remove just some of the images by
first selecting them, and then clicking the button.
You can influence the slice spacing of the interleaved image by the setting of the
check-box:
Now click on the button to do the
interleaving. If you have chosen to save the result to disk, then a
File Chooser will pop up, prompting
you to choose a file name for the new image. Otherwise, the result
will be loaded into Jim.
Set the dimensionality required in the output image using the appropriate
button:
If the result is multiple new images, these will automatically be saved to
disk, regardless of the setting.
Select the image(s) whose dimensionality is to be changed by clicking on the
on the button. This will bring up a
File Chooser from which you can select
one or more input images. To select more than one image file, press the
"Control" key down while making your selection. To select all files
in a list, select one file at the top of the list, press the
"Shift" key down, and select a file at the bottom of the list.
You can select any files from the list in this way.
You can add further images to the list of images by
clicking on the button at any time.
Ensure that the images are in the order in which you want them end up
in the final image(s). If they are not in the right order, select one or more
images in the displayed list to move, and the click either the button or button to get them in the right order.
You can remove all the images from the list by clicking the button, or remove just some of the images by
first selecting them, and then clicking the button.
Now click on the
button to do the dimensionality change. If you have chosen to save the result to disk, or if
the result of the dimensionality change will be more than one image, then a
File Chooser will pop up, prompting
you to choose a base name for the newly-created image(s). Otherwise, the result
will be loaded into Jim.
If you reduce the dimensionality, and the result is therefore multiple output
images, the images will be named
For each of the three colour channels (red, green and blue) of the output image:
If you have chosen to save the result to disk, then a
File Chooser will pop up, prompting
you to choose a file name for the new colour image. Otherwise, the result
will be loaded into Jim.
For each of the two complex components (real & imaginary, or magnitude and phase) of the output
image, set the approriate input image in the image selection panels below.
Note: if you select "Magnitide & Phase", the phase image can be in one of two forms:
If you find the phase values in the resulting Complex image are reversed compared to what you
expect or need (perhaps because alternating echoes in an MRI pulse sequence have phase reversal),
then you can select:
If you have chosen to save the result to disk, then a
File Chooser will pop up, prompting
you to choose a file name for the new Complex image. Otherwise, the result
will be loaded into Jim.
If the result is a single new image (3-D or 4-D) the
new image can either be saved to disk, or loaded into Jim
depending on your selection:
If the result is multiple 3-D images, these will automatically be saved to
disk, regardless of the setting.
Select the image(s) to be de-mosaiced by clicking on the
on the button. This will bring up a
File Chooser from which you can select
one or more input images. To select more than one image file, press the
"Control" key down while making your selection. To select all files
in a list, select one file at the top of the list, press the
"Shift" key down, and select a file at the bottom of the list.
You can select any files from the list in this way.
You can add further images to the list of images by
clicking on the button at any time.
Ensure that the images are in the order in which you want them end up
in the final image(s). If they are not in the right order, select one or more
images in the displayed list to move, and the click either the button or button to get them in the right order.
You can remove all the images from the list by clicking the button, or remove just some of the images by
first selecting them, and then clicking the button.
You can either set the layout (layout of individual slices in the mosaic manually, or you can have
Jim make a guess at the layout. To have Jim guess the mosaic layout, select the
check-box. To do it manually, unselect
"Auto configuration", and the set the number of rows and columns of slices in the mosaic using the
and spinners. You do not have to take all the slices from the mosaic and copy
them to the output image: you can select only the slices you want. In the grid
showing the individual slices in the mosaic in the example below, slices 1,2,15 and 16 have been
de-selected (by clicking on the square on the grid) so that the de-mosaiced image will contain
only slices 3-14.
Now click on the button to do the
de-mosaic. If you have chosen to save the result to disk, or if
the result of the de-mosaic will be more than one image, then a
File Chooser will pop up, prompting
you to choose a base name for the newly-created image(s). Otherwise, the result
will be loaded into Jim.
If you chose to create multiple 3-D output images, the images will be named
The Image Interleaver Tool
Selecting Image Interleaver
from the Organise
menu
of the main display
frame brings up the Image Interleaver Tool:
The Image Interleaver tool takes multiple input images and
interleaves their slices to form a new image with the same number
of slices as all the input images combined. For example, if we
have three input images, a
, b
and
c
,
the new output image will have slices in the order
a1,b1,c1,a2,b3,c2,a3,b3,c3
etc.,
where
a1
is the first slice from image
a
,
b1
is the first slice from image
b
, and
c1
is the first slice from image
c
etc.
The new image will be of
the same type as the first input image. The
new image can either be saved to disk, or loaded into Jim
depending on your selection:
The Dimensionality Changer Tool
Selecting Image Dimensionality Changer
from the Organise
menu
of the main display
frame brings up the Dimensionality Changer Tool:
The Dimensionality Changer tool takes one or more input images and
changes their dimensionality to that required. The result can be one or more
images, depending one whether the dimensionality is increased or decreased:
BaseName1
, BaseName2
,
BaseName3
, BaseName4
etc., where BaseName
is the name you chose above. If you increase the dimensionality and the result
is therefore a single output image, the image will be named BaseName
.
The To RGB Tool
Selecting To RGB
from the Organise
menu
of the main display
frame brings up the To RGB Tool:
The To RGB tool takes three input greyscale images and produces a single colour output
image, with the three colour components (red, green and blue) coming from the three input images.
This provides a way to combine and visualise the information from three separate images.
Each of the three input images must have the same dimensions (number of columns, row and slices of
pixels) in order that they can be combined. In order to achieve this, you may need to
resample, or register them.
When you have set the three input images, and selected the intensity range for each colour
channel, press the button.
The result is a single colour output image, which can can either be saved to disk, or loaded
into Jim
depending on your selection:
The To Complex Tool
Selecting To Complex
from the Organise
menu
of the main display
frame brings up the To Complex Tool:
The To Complex tool takes two input greyscale images representing the complex components,
and produces a single complex output image with a pixel data type of Complex.
Each of the two input images must have the same dimensions (number of columns, row and slices of
pixels) in order that they can be combined. The To Complex tool can combine either
separate images of the real and imaginary parts of the complex image, or the magnitude and phase
values of the complex image. Select which components you want to combine by selecting the
appropriate button:
Jim is able to automatically detect what sort of phase image you are using as input and
apply the appropriate scaling to generate Complex output pixel values.
The De-Mosaic Tool
Selecting De-Mosaic
from the Organise
menu
of the main display
frame brings up the De-Mosaic Tool:
The De-Mosaic tool takes one or more input images that contain mosaics of Siemens images
(multiple images covering the whole head, usually created in fMRI studies) in a single slice.
It de-mosaics them and creates multi-slice images where each real image slice has a slice of its
own. The dimensionality of the de-mosaiced output image(s) is set using the appropriate button:
button:
Select:
BaseName1
, BaseName2
,
BaseName3
, BaseName4
etc., where BaseName
is the name you chose above.