afni的3dTshift报错:WARNING: dataset is already aligned in time!output dataset is just a copy of input!

本文介绍使用3dTshift处理MRI数据时遇到的问题及解决方案。当数据缺失层间时间信息时,程序会发出警告并直接复制输入数据作为输出。解决方法是通过-tpattern选项指定切片时间排列方式。

3dTshift处理数据时,如果该数据里不包含每一层图像采集的时间信息,那么将无法进行层间时间校正,
即出现以下警告:

++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Apr 22 2015) [64-bit]
 *+ WARNING: dataset is already aligned in time!
 *+ WARNING: ==>> output dataset is just a copy of input dataset

解决办法:3dTshift增加-tpattern 选项,告诉程序,切片时间是如何排列的。

 For example if nz = 5 and TR = 1000, then the inter-slice
  time is taken to be dt = TR/nz = 200.  In this case, the
  slices are offset in time by the following amounts:

             S L I C E   N U M B E R
   tpattern    0   1   2   3   4   Comment
   --------- --- --- --- --- ---   -------------------------------
   altplus     0 600 200 800 400   Alternating in the +z direction
   alt+z2    400   0 600 200 800   Alternating, but starting at #1
   altminus  400 800 200 600   0   Alternating in the -z direction
   alt-z2    800 200 600   0 400   Alternating, starting at #nz-2 
   seqplus     0 200 400 600 800   Sequential  in the +z direction
   seqminus  800 600 400 200   0   Sequential  in the -z direction

  If @filename is used for tpattern, then nz ASCII-formatted numbers
  are read from the file.  These indicate the time offsets for each
  slice. For example, if 'filename' contains
     0 600 200 800 400
  then this is equivalent to 'altplus' in the above example.
  (nz = number of slices in the input dataset)

备注:利用dcm2niix将 DICOM 图像转化为nii时,查看.json文件可知,每个TR中层面时间信息。

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