Академический Документы
Профессиональный Документы
Культура Документы
See SPM12_manual.pdf
for general information and
more details for the particular
processing steps.
original document by Thomas P.K. Breckel for HWK Summerschool (Delmenhorst, 2012)
adapted by Anja Gieseler for SPM12 (2015)
Overview
Realignment 5
Coregistration 1 6
Coregistration 2 7
Segmentation 8
Normalisation functional images 9
Normalisation structural images 10
Smoothing 11
Save and run 12
2
Annotation: Existing and virtual files Dependencies
In many processing steps SPM needs When establishing a longer batch (with more
paths and filenames of data which than one processing step), later processing
can be manually selected. steps have to access data that has not yet
been created, which makes manual selection
of this data impossible.
3
DICOM Import
DICOM images
(from CD/DVD or folder)
Output directory
(create one for each subject)
4
Preprocessing: Realignment
Other options:
With Realign: Estimate only the motion parameters will be estimated; no reslicing takes place.
With Realign: Write images get only resliced; motion parameters are needed (as e.g. estimated by Realign: Estimate). 5
Preprocessing: Coregistration 1
meanf*.nii
(Reference image stays unchanged;
meanf* is output from realignment)
Dependency:
Realign: Estimate & Reslice: Mean Image
s*.nii
(Source image will be shifted:
Structural T1-image)
With Coreg: Estimate shifting parameters are stored in the headers of the images and will be applied in the next reslicing step,
which will be conducted during normalisation in the current example.
Reslicing is not necessary in this step. 6
Preprocessing: Coregistration 2 (optional but recommended)
single_subj_T1.nii
(found in spm12 folder: …/spm12/canonical/)
s*.nii
(same image as for coregistration 1)
Other Images:
rf*.nii
(Important: functional images should
also be shifted in the same way as
the source image (structural image))
Dependency:
Realign: Estimate & Reslice: Resliced
Images
and
Realign: Estimate & Reslice: Mean Image
The second coregistration is for support of the segmentation/normalisation procedure. If measurement field or head placement
of the subject during data acquisition was odd, segmentation/normalisation could fail otherwise. Alternatively odd images can
be manually adjusted before, which would make the second coregistration unnecessary (see last slide of this manual).
7
Preprocessing: Segmentation
s*.nii
(coregistered structural T1-image;
previous coregistration cannot be
seen in file-name)
Deformation Fields:
Select Forward
8
Preprocessing: Normalisation functional images
y_s*.nii
(output from segmentation)
Dependency:
Segment: Forward Deformations
- rf*.nii
(realigned functional images)
- meanf*.nii
(if needed; optional)
Dependency:
Realign: Estimate & Reslice: Resliced Images
and optional
Realign: Estimate & Reslice: Mean Image
Alternative: Normalise: Estimate and Normalise Estimate & Write can be used to avoid segmentation and to use standard template
normalisation instead (Images can be matched to a standard MNI-templates provided by SPM without tissue segregation). 9
For Normalise: Write normalisation parameters are needed, as received from prior segmentation step in the current example.
Preprocessing: Normalisation structural image
Dependency:
Segment: Forward Deformations
s*.nii / ms*.nii
(structural or mean corrected
structural image (output from segmentation);
or both images)
Dependency:
Segment: Bias Corrected
(for mean corrected T1-image)
or use no dependency and select
unchanged s*.nii T1-image
Interpolation:
4th Degree B-Spline
1
Preprocessing: Smoothing
wrf*.nii
(realigned and normalised functional
images)
Dependency:
Normalise: Write: Normalised Images
(Attention: With two normalisation steps in a
batch (as in this example) there are two options
for Normalised Images. Choose the one in which
the functional images were normalised. In this
example it is the upper/first normalisation step.)
8 mm smoothing kernel is
recommended and used
in most studies; for activations
in smaller brain regions smaller
kernels (5 or 6 mm) can achieve
better results.
11
Save and run
Save batch
(can also be saved as a script file; useful
to generate a template for scripted
batch generation when working with many
subjects)
12
Attachment: Adjusting odd images manually - support for normalisation processing
Example T1 image
2)
Display Image
1) Adjust rotation (see figure)