[Brains-users] Too few grey matter plugs found

[Ian Malone]

Hi,

I'm trying to follow through the Brains2 standard workup, with T1 scans 
only.  I keep running into the following problem when running tissue 
classification:
"Failure occured (-1): Too few grey matter plugs found, 
{CubicCentimeters 0.000000000000000} CC"

I've tried several different T1 with the same result, using both the MR5 
and MR6 settings for the reslicing. The only time I've successfully run 
tissue classification was with the MNI 152 brain.  Other scans fail, 
both with venous blood traces only and with basal grey and white matter 
traces.  The above error will follow a series of steps reporting k-means 
errors as follows:

Remark:  min gm plugs == 4000
Remark:  min wm plugs == 2000
Remark:  min csf plugs == 200
b2 generate class-plugs i1 {gm wm csf} {{80.186111 113.979065 30.087282 
10.8}} m1 r= patid n= 4000 c= 0.85 p= 0.10 mo= 2.5 vo= 10.0 ps= 2.0 dx= 
1 dy= 1 dz= 1 gm= 4000 wm= 2000 csf= 200 pb= m4
Diagnostic:  bk_generateClassPlugs entered.
Diagnostic:  pv_plugCluster entered.  numClasses == 3
Diagnostic: plug dimensions  = 2 x 2 x 2,  plug volume = 8.000 voxels
Diagnostic: Random Number generator seed = 1769234800
Diagnostic: enclosing box is 69..186 x 82..192 x 15..176
Diagnostic: brain mask has 845974 voxels
Diagnostic: Image set plug variance table:  0 (10.800)
Diagnostic: chunk_z 15..176
Diagnostic: chunk_y 82..192
Diagnostic: chunk_x 69..186
Diagnostic: initial count1 = 849090 ,  oldcount1 = 845974
Diagnostic: max_points = 119999 ,  numplugs = 4014
Diagnostic: count1 = 849090,  count = 0,  sumplugs = 4014
Diagnostic: desired =  4014,  pick_from = 211,  band = 5
Diagnostic: desired =  1819,  pick_from = 211,  band = 10
Diagnostic: HARVESTED 5648 plugs in chunk 15..176 x 82..192 x 69..186.
Table of initial centers:
Class 1:  80.186
Class 2:  113.979
Class 3:  30.087
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1:  32.042
Class 2:  32.042
Class 3:  32.042
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic:  =====>  map of class mean order statistics failed 
to resolve the desired number of classes!
Diagnostic: Center Table
Diagnostic: Center Table
Diagnostic: Center Table


Can anyone suggest what might be going wrong?

Thanks for your time,
Ian

-- 
Ian Malone
Research Associate
Dementia Research Centre
UCL
Institute of Neurology
Queen Square
London WC1N 3BG