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The concept of coregistration is discussed further below. This step needs to be done once before any other pre-processing is done. Coregistration refers to the spatial alignment of a series of images. The subject's T1 anatomical image needs to be coregistered to the T1 template at the start of pre-processing the scan data. Further coregistration is done later on in the process, using images from each run of the scan.
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 1.  1. For the reference image, navigate to the following path: Documents --> MATLAB --> spm8 --> templates, and select the T1.nii file.
 1. For the source image, navigate to the folder containing the subject's T1 anatomical image (labelled mprage), and select the image file.
 1. Leave all the other settings as they are, save and run the batch.
 1. The newly coregistered image should be saved in the mprage folder.
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The first step in statistical parametric mapping is realignment (aka motion correction). This step registers all the images of a specified run from one subject to each other, and gives us information regarding how much the subject moved their head during the scan. This information is later used to ensure that functional images are accurately mapped onto structural ones. The next step is realignment (aka motion correction). This step registers all the images of a specified run from one subject to each other, and gives us information regarding how much the subject moved their head during the scan. This information is later used to ensure that functional images are accurately mapped onto structural ones.
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 1. Under "Reslice Options," the "Resliced Images" option should be changed to "Mean Image only". The rest of the options can be left as they are.  1. Under "Reslice Options," the "Resliced Images" option should be changed to "Mean Image only". The rest of the options can be left as they are. Save and run the batch.
 1. Repeat for all images in each run of the scan.
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Coregistration refers to the spatial alignment of a series of images. This step of coregistration is slightly different from the one completed previously; here, we coregister each image of a run to the coregistered image we generated earlier.

 1.

The official website for SPM can be found here.

This page describes the processes used to analyse fMRI data using SPM in its GUI mode.

DICOM Conversion

COREGISTERING ANATOMICAL TO TEMPLATE

Coregistration refers to the spatial alignment of a series of images. The subject's T1 anatomical image needs to be coregistered to the T1 template at the start of pre-processing the scan data. Further coregistration is done later on in the process, using images from each run of the scan.

  1. On the SPM menu, click "Coregister," and from the drop-down menu select "Est and Res" (estimate and reslice).

  2. For the reference image, navigate to the following path: Documents --> MATLAB --> spm8 --> templates, and select the T1.nii file.

  3. For the source image, navigate to the folder containing the subject's T1 anatomical image (labelled mprage), and select the image file.
  4. Leave all the other settings as they are, save and run the batch.
  5. The newly coregistered image should be saved in the mprage folder.

REALIGNMENT

The next step is realignment (aka motion correction). This step registers all the images of a specified run from one subject to each other, and gives us information regarding how much the subject moved their head during the scan. This information is later used to ensure that functional images are accurately mapped onto structural ones.

  1. On the SPM menu, click "Realign," and from the drop-down menu, select "Est and Res".
  2. Under the "Data" heading, use the "Session" file selector to select all the converted DICOM files of the specified run for the subject.
  3. For "Estimation options," "Quality" controls the quality of the images generated, on a range of 0 to 1. The "Interpolation" option also increases quality of images, with higher degree B-Spline options producing higher quality images. This should be changed to a minimum of "4th Degree B-Spline." The rest of the "Estimation Options" can be left as they are.
  4. Under "Reslice Options," the "Resliced Images" option should be changed to "Mean Image only". The rest of the options can be left as they are. Save and run the batch.
  5. Repeat for all images in each run of the scan.

COREGISTRATION

This step of coregistration is slightly different from the one completed previously; here, we coregister each image of a run to the coregistered image we generated earlier.

rapwiki: StatisticalParametricMapping (last edited 2016-07-15 19:03:43 by RafayKhan)