help > RE: discrepancy between the results of MRIcron V2012 and V2019
Sep 2, 2020  07:09 AM | Chris Rorden
RE: discrepancy between the results of MRIcron V2012 and V2019
Your atlas is not orthogonal to the image plane, as can be seen by the angulation:

fslhd natbrainlab.nii
  sto_xyz:1 -1.000000 -0.000159 0.000962 77.945053
  sto_xyz:2 -0.000160 0.999999 -0.001155 -111.876495
  sto_xyz:3 0.000962 0.001155 0.999999 -50.143166

In MRIcron go to preferences and turn off "Reorient images when loading" to load in native space rather than reslicing. Open your continuous image that has been been resliced to match the template
  https://github.com/rordenlab/spmScripts/blob/b0d8001ae97e28e662f2052751669bdb7e4bc68e/nii_reslice_target.m
Use MRIcron to compute volumes:

Index Name numVox numVoxNotZero fracNotZero
0 0 3628098 624 0.000
1 1 4875 23 0.005
6 6 46399 2 0.000
7 7 6672 2 0.000
8 8 27876 412 0.015
12 12 11032 55 0.005
13 13 10078 92 0.009
16 16 7310 36 0.005
101 101 5298 89 0.017
102 102 8372 24 0.003
103 103 391 14 0.036
107 107 5071 30 0.006
108 108 22061 488 0.022
111 111 13929 1 0.000
112 112 12566 514 0.041
113 113 17470 144 0.008
116 116 7525 338 0.045

Do the same with Matlab (see attached script)

116 regions in /Users/chris/Downloads/tst/natbrainlab.nii,1
region nZero nPos nNeg nNotFinite mn
0 3627474 0 624 0 -0.00024788
1 4852 0 23 0 -0.00107998
6 46397 0 2 0 -2.99442e-07
7 6670 0 2 0 -3.63876e-08
8 27464 0 412 0 -0.0208179
12 10977 0 55 0 -0.00367871
13 9986 0 92 0 -0.00782235
16 7274 0 36 0 -0.00378585
101 5209 0 89 0 -0.0358616
102 8348 0 24 0 -0.001553
103 377 0 14 0 -0.0221525
107 5041 0 30 0 -0.0110846
108 21573 0 488 0 -0.0314722
111 13928 0 1 0 -5.84004e-07
112 12052 0 514 0 -0.0757793
113 17326 0 144 0 -0.0103095
116 7187 0 338 0 -0.102179

Note the results are the same.
Attachment: roi_count.zip

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TitleAuthorDate
Ardalan Aarabi Sep 2, 2020
Chris Rorden Sep 2, 2020
Ardalan Aarabi Sep 2, 2020
RE: discrepancy between the results of MRIcron V2012 and V2019
Chris Rorden Sep 2, 2020