Hi,
I'm running into a problem where using 3dcopy to convert a .nii file into an BRIK causes a loss of slice timing offset information so that 3dTshift returns a message indicating the file is already slice time aligned.
Checking the message board it appears the issue was resolved in 2006 but.....
We're collecting 8 slices every 500 ms for a total of 3024 volumes.
Here is the output of 'nifti_tool -disp_hdr -in_files CSEA_LK_FUNC_4_1.nii':
header file 'CSEA_LK_FUNC_4_1.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 4 112 112 8 3024 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 1.607143 1.607143 8.0 0.5 0.0 0.0 0.0
vox_offset 108 1 352.0
scl_slope 112 1 3.86105
scl_inter 116 1 0.0
slice_end 120 1 7
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 2.5.3
aux_file 228 24
qform_code 252 1 1
sform_code 254 1 0
quatern_b 256 1 -0.5
quatern_c 260 1 0.5
quatern_d 264 1 -0.5
qoffset_x 268 1 -18.384617
qoffset_y 272 1 91.521736
qoffset_z 276 1 114.849495
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
Any ideas as to why the slice timing information is not being preserved when converting to a BRIK?
Thanks,
Vinny
