3dinfo and slice timing

AFNI Message Board
1

hello,
I’m trying to figure out where I can get the information regarding slice timing in the EPI file.

the -VERB option in 3dinfo doesn’t provide this info, and if I try to add -slice_timing I get a series of 0s out.

Any idea of what’s happening? I’d like to know from the EPI the acquisition characteristics to use in 3dTshift.

thank you,
ns

2

Hi ns,

Those are the right commands to use.

It looks like the dataset has no slice timing information. How was the dataset created?

  • rick
3

I’m trying to read the header of nii files created from a 3T Philips scanner

4

What does “nifti_tool -disp_hdr -infile IMAGE.nii” show for that IMAGE file?

  • rick
5

This is what I get from that command:

N-1 header file ‘subj1.nii’, num_fields = 43

all fields:
name offset nvals values

sizeof_hdr 0 1 348
data_type 4 10
db_name 14 18
extents 32 1 0
session_error 36 1 0
regular 38 1
dim_info 39 1 0
dim 40 8 4 80 80 53 110 1 1 1
intent_p1 56 1 0.0
intent_p2 60 1 0.0
intent_p3 64 1 0.0
intent_code 68 1 0
datatype 70 1 4
bitpix 72 1 16
slice_start 74 1 0
pixdim 76 8 1.0 2.25 2.25 3.5 3.0 0.0 0.0 0.0
vox_offset 108 1 352.0
scl_slope 112 1 33.900368
scl_inter 116 1 0.0
slice_end 120 1 52
slice_code 122 1 0
xyzt_units 123 1 10
cal_max 124 1 0.0
cal_min 128 1 0.0
slice_duration 132 1 0.0
toffset 136 1 0.0
glmax 140 1 0
glmin 144 1 0
descrip 148 80 Philips Medical Systems Achieva 3.2.1
aux_file 228 24
qform_code 252 1 1
sform_code 254 1 0
quatern_b 256 1 -0.0
quatern_c 260 1 0.707107
quatern_d 264 1 -0.707107
qoffset_x 268 1 93.0
qoffset_y 272 1 92.00354
qoffset_z 276 1 102.0
srow_x 280 4 1.0 0.0 0.0 0.0
srow_y 296 4 0.0 1.0 0.0 0.0
srow_z 312 4 0.0 0.0 1.0 0.0
intent_name 328 16
magic 344 4 n+1

6

Hi,

Two fields that ought to be populated here are slice_code and slice_duration. While slice duration might not be necessary (one could default to TR/nslices), slice code should be set (to provide the slice acquisition order). In some cases the slice_code will not have a possible value to correspond with the slice order (NIFTI cannot support arbitrary slice timing). What was the slice timing in this case? Was this a multi-band acquisition?

If you know the slice timing, it is possible to pass it separately, which would allow for a timing that NIFTI cannot represent.

  • rick