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MayaSa
May 20, 2023 07:36AM
Hi,
I used proc.py with m_tedana to preprocess my 3T ME data, and encountered an artifact for one of the runs (attached).
I tried converting again the dicom files into afni files, and noticed some errors: 

*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center     :      -9.25262      -18.9084       2.79301
Slice-based Center:      -8.04193      -17.6613       2.91659
++ Command line TR=2s ; Images TR=2s
-- using Siemens slice timing (50) : 0.000 1.030 0.080 1.110 0.160 1.190 0.238 1.268 0.318 1.348 0.398 1.428 0.475 1.505 0.555 1.585 0.635 1.665 0.713 1.743 0.793 1.823 0.873 1.903 0.950 0.000 1.030 0.080 1.110 0.160 1.190 0.238 1.268 0.318 1.348 0.398 1.428 0.475 1.505 0.555 1.585 0.635 1.665 0.713 1.743 0.793 1.823 0.873 1.903 0.950
++ Checking for time series outliers
 
to3d WARNING:
Significant outliers detected in these sub-bricks:
   9  10  20  21  22  23  24  25  27  28  30  31
  35  44  45  51  58  60  63  65  66  70  73  77
  79  81  82  83  87  88  91  92  94  96  99 101
 102 103 114 120 125 129 136 140 142 148 149 150
 151 152 153 154 155 156 157 158
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.  ]

Do you know what causes this artifact, and how can I solve it?
Thank you,
Maya
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Subject Author Posted

preprocessing problem Attachments

MayaSa May 20, 2023 07:36AM

Re: preprocessing problem

MayaSa May 21, 2023 04:17AM