Organising Your Images

Jim has five tools to help you get the best out of your images.

• Slice Extractor. Allows you to select particular slices from a multi-slice image to produce a new multi-slice image.
• Image Concatenator. Pastes several multi-slice images end-to-end to create a new multi-slice image with all the slices from all the images.
• Image Interleaver. Interleaves the slices from several multi-slice images.
• Dimensionality Changer. Changes the dimensionality of one or more multi-slice images.
• De-Mosaic. De-Mosaics Siemens images images stored in the mosaic format.

  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 creates 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:
  • Regular steps. Step through the image with the specified step size.

    

    In the example above, every third slice is extracted. The start and end slices are specified in the Slice Range fields.

    

    By default, the first slice is 1, and the last slice if the number of slices in the input image. In the example above, slice extraction would start at slice 5, and continue to the end of the image in steps of 3.

    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.

  • Odd- or Even-numbered slices. Extract odd-numbered or even-numbered slices between the ranges specified in the Slice Range.

    

  • Numbered slices. A list of slices and slice ranges is specified as a comma (,) separated list:

    

    In the example above, slices 5, 7, 13, 20, 21, 22, 23, 24, 25 and 3 will be extracted from the input image. Note that a range of slices is specified using a hyphen as in the example above. Note also that the slices can be specified in any order, and the output image will be assembled in that order.

    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.

  

  Now click on the button to do the extraction. 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.

  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.

  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:

  

  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:

  • If the check-box is not selected, the slice spacing of the interleaved image will be equal to the slice spacing of the first input image divided by the number of interleaved images.
  • If the check-box is selected, the slice spacing of the interleaved image will be the same as that of the first input image.

  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.

  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:
  • If the dimensionality is increased (for example, creating a 4-D image from several 3-D images), the result will always be a single image of the requested dimensionality.
  • If the dimensionality is decreased (for example, creating a several 2-D images from a single 3-D image), the result will always be a multiple images of the requested dimensionality.
  Set the dimensionality required in the output image using the appropriate button:

  

  Any new image will be of the same type as the first input image encountered. If the result is a single new image (dimensionality increased) the new image can either be saved to disk, or loaded into Jim depending on your selection:

  

  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 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 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:
  • One 3-D image if you want the resulting de-mosaiced image to be a single 3-D image containing all de-mosaiced slices from all input images.
  • Multiple 3-D images (one per time point) if you want the resulting de-mosaiced image to be a multiple 3-D images, one per 3-D image per mosaic.
  • One 4-D image if you want the resulting de-mosaiced image to be a single 4-D image with multiple volumes, with one time-point per mosaic.

  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.

  

  If you selected "Auto configuration", Jim will automatically not include any slices of the that contain no image data.

  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 BaseName1, BaseName2, BaseName3, BaseName4 etc., where BaseName is the name you chose above.

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