关于DPARSFA 2.1新增功能的疑问

Submitted by wleewell on Mon, 07/02/2012 - 12:39

看了DPARSFA 2.1的新增功能后有以下疑问，望严老师指点。

主要是关于这一段话：

Normalize by DARTEL has been added. Details: (1) "T1 Coreg to Fun": the individual structural T1 image is coregistered to the mean functional image after motion correction. (2) "New Segment + DARTEL": New Segment -- The transformed structural image is then segmented into gray matter, white matter and cerebrospinal fluid by using "New Segment" in SPM8. (3) "New Segment + DARTEL": DARTEL -- Create Template, and DARTEL -- Normalize to MNI space (Many Subjects) for GM, WM, CSF and T1 Images (unmodulated, modulated and smoothed [8 8 8] kernel versions). (4) "Normalize by DARTEL": DARTEL Normalize to MNI space (Few Subjects) for functional images. (5) "Smooth by DARTEL": DARTEL Normalize to MNI space (Few Subjects) for functinal images but with smooth kernel as specified, the smoothing is part of the normalisation to MNI space computes these average intensities from the original data, rather than the warped versions.

Questions：
关于Checkbox "Reorient Fun*"模块： 在dcm2nii DICOM to N

Forums:

YAN Chao-Gan

Tue, 07/03/2012 - 21:01

1. 不会有这个问题。因为Reorient Fun是在Slice timing以及realignment之后的步骤，不会影响slice timing correction. 将功能像和结构像分别手动reorient到一个较好位置，有助于提高coregistration和normalization的准确度。

2. 推荐用New Segment+DARTEL。目前SPM组比较推荐这种方式。另外，也有一篇文章进行了评估：

Klein, A., Andersson, J., Ardekani, B.A., Ashburner, J., Avants, B., Chiang, M.C., Christensen, G.E., Collins, D.L., Gee, J., Hellier, P., Song, J.H., Jenkinson, M., Lepage, C., Rueckert, D., Thompson, P., Vercauteren, T., Woods, R.P., Mann, J.J., Parsey, R.V., 2009. Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. Neuroimage 46, 786-802.

3. 我的理解：Many Subjects是在DARTEL中指结构像，每个被试只有少数图像。Few Subjects是每个被试都有很多个时间点（很多图像）。

4. Reorient after coreg interactively. 在coreg之后，如果图像没有一个好的orientation，则后续的segment和DARTEL有可能效果不好。当然，如果你已经分别对功能像和结构像进行了reorient，则不用选这一步。

5. 8mm的平滑核是针对结构像的。这个参数我没有留出来自由设置。后面可以自由设置的平滑核都是针对功能像的。