AFNI Gurus-
I'm working with data from another site and have a couple of questions regarding how DIMON handles slice timing information.
On some of the newer collected data, output from Dimon shows that it is using a Siemens timing of alt+z2. The log sheet that was filled out when the data was collected says the data was collected in Altplus (alt+z). Is Dimon correct? Dimon output below.
All data collected on either a 1.5 or 3T Siemens scanner in mosaic DICOM.
Dimon running, use <ctrl-c> to quit...
-- scanning for first volume
-- checking 156 potential DICOM files... 00%++ Data detected to be oblique
*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center : -1.03357 -9.35348 13.5651
Slice-based Center: 0.685173 -7.66985 13.2195
-- Siemens timing (32 entries): 1.005 0.000 1.067 0.062 1.130 0.128 1.193 0.190 1.255 0.252 1.318 0.315 1.380 0.378 1.445 0.440 1.508 0.502 1.570 0.565 1.633 0.628 1.695 0.690 1.758 0.753 1.820 0.818 1.883 0.880 1.945 0.943
++ DICOM WARNING: no more Slice_Spacing messages will be printed
100%
++ found 156 DICOM files
-- dicom sort : 0 inversions, 0 non-DICOM files, sort type 0x10
(dicom_org was unnecessary)
-- first volume found (1 slices)
-- scanning for additional volumes...
-- run 8: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156
final run statistics:
volume info :
slices : 1
z_first : -25.4
z_last : -25.4
z_delta : 4
oblique : yes
mos_nslices : 32 (mosaic)
run # 8 : volumes = 156, first file (#0) = s8_ep2d_bold_156/MR.1.3.12.2.1107.5.2.32.35407.2012120516201732212646472
++ to3d: AFNI version=AFNI_2011_12_21_1014 (Dec 6 2012) [64-bit]
++ Authored by: RW Cox
++ Counting images: total=4992 2D slices
++ DICOM NOTICE: 6x6 Siemens Mosaic of 32 64x64 images in file s8_ep2d_bold_156/MR.1.3.12.2.1107.5.2.32.35407.2012120516201732212646472
++ Data detected to be oblique
++ Each 2D slice is 64 X 64 pixels
++ Voxel dimensions: 3.4375 X 3.4375 X 4.0000 mm
++ Image data type = short
++ Reading images:
++ DICOM NOTICE: 6x6 Siemens Mosaic of 32 64x64 images in file s8_ep2d_bold_156/MR.1.3.12.2.1107.5.2.32.35407.2012120516201932165246570
++ DICOM WARNING: no more Slice_Spacing messages will be printed
..........................................
*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center : -1.03357 -9.35348 13.5651
Slice-based Center: 0.685173 -7.66985 13.2195
++ Command line TR=2s ; Images TR=2s
-- using Siemens slice timing (32) : 1.005 0.000 1.067 0.062 1.130 0.128 1.193 0.190 1.255 0.252 1.318 0.315 1.380 0.378 1.445 0.440 1.508 0.502 1.570 0.565 1.633 0.628 1.695 0.690 1.758 0.753 1.820 0.818 1.883 0.880 1.945 0.943
++ Checking for time series outliers
to3d WARNING:
Significant outliers detected in these sub-bricks:
0 1 2 3 4 5 6 11 13 14 15 105
107 113 122 123 124 125 126 127 128 129 130 131
132 133 134 135 136 137 138 139 140 141 143 146
You should inspect the dataset for possible corruption.
[Outliers are defined as in program 3dToutcount. ]
[Outliers early in an EPI time series may be due to ]
[the longitudinal magnetization equilibration effect.]
[Other causes are subject movement, scanner problems,]
[or anything that makes a time series look irregular.]
[ 3dToutcount -save outnam dataset | 1dplot -stdin ]
[can be used to make a dataset 'outnam' that marks ]
[outlier voxels; see 3dToutcount -help for details. ]
++ 3D dataset written to disk
Edited 4 time(s). Last edit at 12/18/2012 04:53PM by Peter Molfese.
