Slice Timing

Submitted by YAN Chao-Gan on

Most fMRI data are acquired using two-dimensional pulse sequences that acquire images one slice at a time, thus all slices are acquired at different time within a repeat time (TR). Timing differences are especially problematic for longer TR. Hence the differences in image acquisition time between slices need to be corrected.

Of note: The latest version of DPABISurf/DPARSF will read the slice timing information from DICOM files. If you are starting with DICOM files, just leave the parameters of number of slices, slice order and reference slice as DEFAULT.

The number of slices, slice order and reference slice need to be specified, then DPARSF will do slice timing by calling functions in SPM.

For batch mode, The slice order type could be specified for each participant into SliceOrderInfo.tsv (under working directory) file, thus allow different slice timing correction for different participants. Please specify Slice Number as 0 in DPARSFA GUI. 

Within SliceOrderInfor.tsv, the first column is Subject ID, and the second column is Slice Order Type. The third column (if available) is the Slice Order Type for Session 2.
SA: sequential ascending
SD: sequential descending
IA: interleaved ascending
ID: interleaved descending
IA2: interleaved ascending, for SIEMENS scanner with even number of slices. Scanning of 2,4,6,... and then 1,3,5,... i.e., [2:2:SliceNumber,1:2:SliceNumber]
ID2: interleaved descending, for SIEMENS scanner with even number of slices. Scanning of [SliceNumber-1:-2:1,SliceNumber:-2:1].
 
Please see {DPARSF}/Docs/SliceOrderInfo.tsv for a sample file. Also, please see Yan et al., 2013 Table 3 for a sample of FCP data (although IA2 and ID2 were not defined in that table.)
 
Yan, C.G., Craddock, R.C., Zuo, X.N., Zang, Y.F., Milham, M.P., 2013. Standardizing the intrinsic brain: towards robust measurement of inter-individual variation in 1000 functional connectomes. Neuroimage 80, 246-262.
 
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A sample of SliceOrderInfor.tsv:
Subject ID Slice Order Type S2: Slice Order Type
MRN_0027412 IA IA
MRN_0027413 IA IA
MRN_0027417 IA IA
MRN_0027418 IA IA
MRN_0027419 IA IA
NKI_TRT_0021001_1400 SliceOrderInfo_NKI1400.txt SliceOrderInfo_NKI1400.txt
NKI_TRT_0021001_2500 IA2 IA2
NKI_TRT_0021001_645 SliceOrderInfo_NKI645.txt SliceOrderInfo_NKI645.txt
NKI_TRT_0021002_1400 SliceOrderInfo_NKI1400.txt SliceOrderInfo_NKI1400.txt
NKI_TRT_0021002_2500 IA2 IA2
NKI_TRT_0021002_645 SliceOrderInfo_NKI645.txt SliceOrderInfo_NKI645.txt
NKI_TRT_0021006_1400 SliceOrderInfo_NKI1400.txt SliceOrderInfo_NKI1400.txt
NKI_TRT_0021006_2500 IA2 IA2
NKI_TRT_0021006_645 SliceOrderInfo_NKI645.txt SliceOrderInfo_NKI645.txt
SWU_4_0025629 IA2 IA2
SWU_4_0025630 IA2 IA2
SWU_4_0025631 IA2 IA2
SWU_4_0025632 IA2 IA2
SWU_4_0025633 IA2 IA2
SWU_4_0025634 IA2 IA2
 
Of note, SliceOrderInfo_NKI1400.txt and SliceOrderInfo_NKI645.txt are slice timing specifications for MultiBand data in NKI Enhanced Rockland Sample.
 

Dear Experts

For batch mode, The slice order type could be specified for each participant into SliceOrderInfo.tsv (under working directory) file, thus allow different slice timing correction for different participants. Please specify Slice Number as 0 in DPARSFA GUI. 

Within SliceOrderInfor.tsv, the first column is Subject ID, and the second column is Slice Order Type. The third column (if available) is the Slice Order Type for Session 2.
SA: sequential ascending
SD: sequential descending
IA: interleaved ascending
ID: interleaved descending
IA2: interleaved ascending, for SIEMENS scanner with even number of slices. Scanning of 2,4,6,... and then 1,3,5,... i.e., [2:2:SliceNumber,1:2:SliceNumber]
ID2: interleaved descending, for SIEMENS scanner with even number of slices. Scanning of [SliceNumber-1:-2:1,SliceNumber:-2:1].
Taking the SliceOrderInfo.tsv for example.
 
Put the file under /Subjects/*.tsv
 
In DPARSF GUI:
 
  1. Slice number as 0 (if "0", detect automatically right?)
  2. Slice order = ? 
  3. Reference slice as 0 (if "0", detect automatically right?)
 
By the way, where could I get the slice number and order type information for ABIDE data sets?
 
Best 
Larry

tangtang1001

Thu, 10/10/2024 - 01:39

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the slice order information for the ABIDE II dataset

Dear Dr. Yan,

I want to preprocess the ABIDE II data, however, i am not quite sure about  the slice order according to the scan parameters of each site on ABIDE site. I found the slice order of ABIDE I that provided on your website.  

I wonder if you have the slice order information for the ABIDE II dataset. If so, would it be possible for you to share it with me? Thank you.

Best wishes,

TANG

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