SPM8手册：时间与空间处理方法详解

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"SPM8 Manual 是由 The FIL Methods Group (包括荣誉成员)撰写的一份详细的指导文档，主要关注于功能磁共振成像（fMRI）处理中的关键步骤。该手册分为两大部分：时序处理和空间处理，旨在帮助用户理解和应用 SPM8 工具进行数据分析。时序处理第1章专门探讨了时间序列校准，这是fMRI分析的基础。内容涵盖了以下几个子部分： 1.1 数据校准：强调了对不同扫描参数如 session、slice数量、重复时间(TR)和回波时间(TA)的精确设置，这些都是确保时间线同步的重要因素。 1.2 片层顺序：解释了在成像过程中如何安排扫描片层以及参考片层的选择，这对于消除因扫描顺序引起的偏差至关重要。 1.3 文件前缀：说明了如何命名和组织数据文件，以便于后续处理。空间处理第二部分着重于图像的空间校准和转换： 2.1 重新对齐（Realign）：这部分详细阐述了数据预处理的第一步，即估计和纠正由于运动或其他因素导致的图像漂移，提供了估计选项和设置。 2.2 重采样（Reslice）：针对不同空间分辨率或空间模板进行图像调整，确保所有数据在一致的坐标系下进行分析。 2.3 重新对齐与重采样结合：介绍了同时执行这两项操作的流程，以及相应的数据和选项设置。 3.0 重新对齐与去扭曲（Realign & Unwarp）：当考虑到头部运动的影响可能进一步导致空间变形时，这一节讲解了如何在去除了头动效应后，对图像进行进一步的校准。这些章节不仅提供了具体的步骤和参数设置，还可能包含关于如何处理各种异常情况、误差检查和优化性能的建议。SPM8 Manual 是功能神经成像研究者和分析者的宝贵资源，通过学习和实践，可以确保在进行fMRI数据分析时得到准确和可靠的脑功能映射结果。"

16 CONTENTS

Chapter 1

Slice Timing

Contents

1.1 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.1.1 Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.2 Number of Slices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.3 TR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.4 TA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.5 Slice order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.6 Reference Slice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

1.7 Filename Preﬁx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Correct diﬀerences in image acquisition time between slices. Slice-time corrected ﬁles are

prepended with an ’a’.

Note: The sliceorder arg that speciﬁes slice acquisition order is a vector of N numbers, where

N is the number of slices per volume. Each number refers to the position of a slice within the

image ﬁle. The order of numbers within the vector is the temporal order in which those slices

were acquired. To check the order of slices within an image ﬁle, use the SPM Display option and

move the cross-hairs to a voxel co-ordinate of z=1. This corresponds to a point in the ﬁrst slice

of the volume.

The function corrects diﬀerences in slice acquisition times. This routine is intended to correct

for the staggered order of slice acquisition that is used during echo-planar scanning. The correction

is necessary to make the data on each slice correspond to the same point in time. Without

correction, the data on one slice will represent a point in time as far removed as 1/2 the TR from

an adjacent slice (in the case of an interleaved sequence).

This routine ”shifts” a signal in time to provide an output vector that represents the same

(continuous) signal sampled starting either later or earlier. This is accomplished by a simple shift

of the phase of the sines that make up the signal. Recall that a Fourier transform allows for a

representation of any signal as the linear combination of sinusoids of diﬀerent frequencies and

phases. Eﬀectively, we will add a constant to the phase of every frequency, shifting the data in

time.

Shifter - This is the ﬁlter by which the signal will be convolved to introduce the phase shift.

It is constructed explicitly in the Fourier domain. In the time domain, it may be described as

an impulse (delta function) that has been shifted in time the amount described by TimeShift.

The correction works by lagging (shifting forward) the time-series data on each slice using sinc-

interpolation. This results in each time series having the values that would have been obtained

had the slice been acquired at the same time as the reference slice. To make this clear, consider

a neural event (and ensuing hemodynamic response) that occurs simultaneously on two adjacent

slices. Values from slice ”A” are acquired starting at time zero, simultaneous to the neural event,

20 CHAPTER 1. SLICE TIMING

while values from slice ”B” are acquired one second later. Without correction, the ”B” values

will describe a hemodynamic response that will appear to have began one second EARLIER on

the ”B” slice than on slice ”A”. To correct for this, the ”B” values need to be shifted towards

the Right, i.e., towards the last value.

This correction assumes that the data are band-limited (i.e. there is no meaningful information

present in the data at a frequency higher than that of the Nyquist). This assumption is support

by the study of Josephs et al (1997, NeuroImage) that obtained event-related data at an eﬀective

TR of 166 msecs. No physio-logical signal change was present at frequencies higher than our

typical Nyquist (0.25 HZ).

When using the slice timing correction it is very important that you input the correct slice

order, and if there is any uncertainty then users are encouraged to work with their physicist to

determine the actual slice acquisition order.

One can also consider augmenting the model by including the temporal derivative in the

informed basis set instead of slice timing, which can account for +/- 1 second of changes in

timing.

Written by Darren Gitelman at Northwestern U., 1998. Based (in large part) on ACQCOR-

RECT.PRO from Geoﬀ Aguirre and Eric Zarahn at U. Penn.

1.1 Data

Subjects or sessions. The same parameters speciﬁed below will be applied to all sessions.

1.1.1 Session

Select images to slice-time correct.

1.2 Number of Slices

Enter the number of slices.

1.3 TR

Enter the TR (in seconds).

1.4 TA

Enter the TA (in seconds). It is usually calculated as TR-(TR/nslices). You can simply enter

this equation with the variables replaced by appropriate numbers.

1.5 Slice order

Enter the slice order. Bottom slice = 1. Sequence types and examples of code to enter are given

below.

ascending (ﬁrst slice=bottom): [1:1:nslices]

descending (ﬁrst slice=top): [nslices:-1:1]

interleaved (middle-top):

for k = 1:nslices,

round((nslices-k)/2 + (rem((nslices-k),2) * (nslices - 1)/2)) + 1,

end

interleaved (bottom -> up): [1:2:nslices 2:2:nslices]

interleaved (top -> down): [nslices:-2:1, nslices-1:-2:1]

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玛丽安

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