[Brains-users] Too few grey matter plugs found

[Greg Harris]

Hi, Ian.

Is there any way you could donate one of the T1-only datasets that is
causing this failure?

The text {{80.186111 113.979065 30.087282 10.8}} gives the expected gray,
white, and csf means for your T1 image, and the expected plug variance.
The first failure of kmeans clustering seems to indicate that your brain
image is not near these numerical estimates. When it continues past the text
> Class 1:  32.042
> Class 2:  32.042
> Class 3:  32.042
This says to me that the mean, max and min in the brain mask (m1) were
identical, so I would also want to examine the brain mask:  why is it all
one intensity in the mask? The text
> Diagnostic: enclosing box is 69..186 x 82..192 x 15..176
gives the bounding box for this mask, so it is not one point or something
like that.  

The text "r= patid" might be causing a problem:  r is the random seed for
the plug picker.  Give it a positive integer, not a variable name.  We use
our patient id solely to make the choice of training class plugs random but
reproducible.

Greg Harris
Iowa Psychiatric Neuroimaging Consortium

On 8/18/08 11:57 AM, "Ian Malone" <ian.malone at drc.ion.ucl.ac.uk> wrote:

> 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