We are currently scanning on a Philips 3T scanner that is giving us multiframe DICOM output.


When we look at doing slice timing correction, I've referenced this document from Bob Cox here:
[nifti.nimh.nih.gov]
This was written a few years back, and I'm not sure if this is correct for multiframe headers however.

It states that:
(snip)
slice_code:
If this value is nonzero (ours is 0)
and if slice_dim is nonzero (field not present)
and if slice_duration is positive (ours is 0.0)
then slice_code indicates the timing pattern of the slice acquisition.
(end snip)

Our data:
name offset nvals values
------------------- ------ ----- ------
slice_duration 132 1 0.0
slice_code 122 1 0

Also see this thread:
[afni.nimh.nih.gov]

Which is likely on the same topic.

Does anyone know the correct slice timing? It appears as if it is simply sequential, but I am uncertain.

Here's the entire output from the nifty Nifti tool:


N-1 header file 'Ncd001_resting.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 r
dim_info 39 1 48
dim 40 8 4 192 192 28 140 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 16
bitpix 72 1 32
slice_start 74 1 0
pixdim 76 8 -1.0 1.197917 1.197917 5.0 1.999999 0.0 0.0 0.0
vox_offset 108 1 5664.0
scl_slope 112 1 0.0
scl_inter 116 1 0.0
slice_end 120 1 27
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
aux_file 228 24
qform_code 252 1 1
sform_code 254 1 1
quatern_b 256 1 -0.0
quatern_c 260 1 1.0
quatern_d 264 1 0.0
qoffset_x 268 1 106.973282
qoffset_y 272 1 -107.441071
qoffset_z 276 1 -10.339375
srow_x 280 4 -1.197917 -0.0 -0.0 106.973282
srow_y 296 4 -0.0 1.197917 -0.0 -107.441071
srow_z 312 4 0.0 0.0 5.0 -10.339375
intent_name 328 16
magic 344 4 n+1

header file 'Ncd001_resting.nii', num_fields = 63, fields:

all fields:
name offset nvals values
------------------- ------ ----- ------
ndim 0 1 4
nx 8 1 192
ny 16 1 192
nz 24 1 28
nt 32 1 140
nu 40 1 1
nv 48 1 1
nw 56 1 1
dim 64 8 4 192 192 28 140 1 1 1
nvox 128 1 144506880
nbyper 136 1 4
datatype 140 1 16
dx 144 1 1.197917
dy 152 1 1.197917
dz 160 1 5.0
dt 168 1 1.999999
du 176 1 0.0
dv 184 1 0.0
dw 192 1 0.0
pixdim 200 8 0.0 1.197917 1.197917 5.0 1.999999 0.0 0.0 0.0
scl_slope 264 1 0.0
scl_inter 272 1 0.0
cal_min 280 1 0.0
cal_max 288 1 0.0
qform_code 296 1 1
sform_code 300 1 1
freq_dim 304 1 0
phase_dim 308 1 0
slice_dim 312 1 3
slice_code 316 1 0
slice_start 320 1 0
slice_end 328 1 27
slice_duration 336 1 0.0
quatern_b 344 1 -0.0
quatern_c 352 1 1.0
quatern_d 360 1 0.0
qoffset_x 368 1 106.973282
qoffset_y 376 1 -107.441071
qoffset_z 384 1 -10.339375
qfac 392 1 -1.0
qto_xyz 400 16 -1.197917 -0.0 -0.0 106.973282 0.0 1.197917 -0.0 -107.441071 -0.0 0.0 5.0 -10.339375 0.0 0.0 0.0 1.0
qto_ijk 528 16 -0.834783 -0.0 -0.0 89.299438 -0.0 0.834783 0.0 89.68994 -0.0 -0.0 0.2 2.067875 0.0 0.0 0.0 1.0
sto_xyz 656 16 -1.197917 -0.0 -0.0 106.973282 -0.0 1.197917 -0.0 -107.441071 0.0 0.0 5.0 -10.339375 0.0 0.0 0.0 1.0
sto_ijk 784 16 -0.834783 -0.0 -0.0 89.299438 -0.0 0.834783 -0.0 89.68994 0.0 -0.0 0.2 2.067875 0.0 0.0 0.0 1.0
toffset 912 1 0.0
xyz_units 920 1 2
time_units 924 1 8
nifti_type 928 1 1
intent_code 932 1 0
intent_p1 936 1 0.0
intent_p2 944 1 0.0
intent_p3 952 1 0.0
intent_name 960 16
descrip 976 80
aux_file 1056 24
fname 1080 1 'Ncd001_resting.nii'
iname 1088 1 'Ncd001_resting.nii'
iname_offset 1096 1 5664
swapsize 1104 1 4
byteorder 1108 1 1
data 1112 1 (raw data of unknown type)
num_ext 1120 1 1
ext_list 1128 1 ecode = 4, esize = 5312, edata = <?xml

analyze header file 'Ncd001_resting.nii', num_fields = 47

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 r
hkey_un0 39 1 48
dim 40 8 4 192 192 28 140 1 1 1
unused8 56 1 0
unused9 58 1 0
unused10 60 1 0
unused11 62 1 0
unused12 64 1 0
unused13 66 1 0
unused14 68 1 0
datatype 70 1 16
bitpix 72 1 32
dim_un0 74 1 0
pixdim 76 8 -1.0 1.197917 1.197917 5.0 1.999999 0.0 0.0 0.0
vox_offset 108 1 5664.0
funused1 112 1 0.0
funused2 116 1 0.0
funused3 120 1 0.0
cal_max 124 1 0.0
cal_min 128 1 0.0
compressed 132 1 0.0
verified 136 1 0.0
glmax 140 1 0
glmin 144 1 0
descrip 148 80
aux_file 228 24
orient 252 1 1
originator 253 5 256 0 0 128 -32768
generated 263 10 ?
scannum 273 10 áÖÂn%ÁUU™
patient_id 283 10 ¿
exp_date 293 10 òÕB
exp_time 303 10 ?
hist_un0 313 3
views 316 1 0
vols_added 320 1 1084227584
start_field 324 1 -1054511596
field_skip 328 1 0
omax 332 1 0
omin 336 1 0
smax 340 1 0
smin 344 1 3222382
header file 'Ncd001_resting.nii', num_ext = 1
ext #0 : ecode = 4, esize = 5312, edata = <?xml version='1.0' ?>
<AFNI_attributes
self_idcode="NII_34QzolKA9TaqXQEkp56nqA"
NIfTI_nums="192,192,28,140,1,16"
ni_form="ni_group" >
<AFNI_atr
ni_type="String"
ni_dimen="1"
atr_name="HISTORY_NOTE" >
"[james@PSY-researchpc: Sat Nov 30 12:33:16 2019] {AFNI_19.3.11:linux_openmp_64} 3drefit -deoblique Ncd001_resting.nii Ncd001_resting2.nii"
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<AFNI_atr
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<AFNI_atr
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1.197917
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</AFNI_atr>

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Kind regards,
James