On tpattern and slice timing

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1

Hi, List experts,

I was wondering whether we can directly get the information from the imaging files on how the fMRI data (i.e.,slices) were acquired. For instance, there are at least four types as following. These days I read papers and realize this question which is always in my mind.

Sequential Ascending: 1,2,3,4,5,6
Sequential Descending: 6,5,4,3,2,1
Interleaved Ascending: 1,4,2,5,3,6
Interleaved Descending: 6,3,5,2,4,1

Further, I am noted that an option “tpattern” is corresponding to this, but I do not know exactly how the relates. Any good pointers?

tpattern = Code word that identifies how the slices (z-direction) were gathered in time.  The values that can be used:

   alt+z = altplus    = alternating in the plus direction
   alt+z2             = alternating, starting at slice #1
   alt-z = altminus   = alternating in the minus direction
   alt-z2             = alternating, starting at slice #nz-2
   seq+z = seqplus    = sequential in the plus direction
   seq-z = seqminus   = sequential in the minus direction
   zero  = simult     = simultaneous acquisition
   FROM_IMAGE         = (try to) read offsets from input images
   @filename          = read temporal offsets from 'filename'

Any advice would be much apprecriated.
Juan

2

Your example orders should match our
seq+z
seq-z
alt+z
alt-z

Note we use a 0-based system for almost everything, so slice 0 is the first slice. You can specify slice timing patterns using to3d, 3dTshift and 3drefit. Search our messageboard for other posts about this topic.

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thank you very much. Daniel.
J