[Camino-users] Connectivity Mapping with Camino

[Gavin Winston]

I am trying to use Camino release 1011 to produce connectivity maps as 
per the tutorial.  However the conmap stage crashes with the following 
error message:

 > conmap -inputfile probab/track.Bdouble -roifile dti/dti_wmparc.nii.gz

(I have changed to code so the boolean silent is false to give more output)

11-Oct-2011 10:48:54 apps.ConnectivityMapping main
INFO: yay! Found Seed file
regions:177
  3011,  1011,  4025,  2025,  2029,  4029,  5002,  5001,  3004,  251, 
4004,  3025,  3021,  1025,  2005,  4005,  4021,  4011,  4013,  43, 
1021,  47,  8,  7,  16,  46,  15,  14,  49,  63,  60,  4031,  4022, 
4024,  4018,  4003,  54,  4030,  4007,  4009,  28,  12,  13,  10,  17, 
1016,  85,  2024,  52,  2017,  4017,  4028,  1024,  3024,  24,  1000, 
3034,  51,  4027,  4020,  2027,  2020,  1012,  1030,  1033,  3033, 
3007,  3030,  3017,  3028,  1028,  1017,  3010,  1010,  2010,  1013, 
1007,  1009,  4015,  2015,  1015,  2007,  2006,  4006,  2009,  2033, 
4033,  18,  26,  1014,  2000,  3029,  1029,  50,  4012,  3006,  2013, 
3023,  4008,  53,  3009,  3008,  2011,  31,  5,  11,  3016,  3012, 
3020,  3027,  1020,  3015,  2030,  2019,  3013,  3001,  4010,  3005, 
1027,  3019,  1019,  4016,  4,  1006,  1022,  3022,  2028,  2022,  2018, 
  44,  2012,  1005,  2021,  4032,  2032,  3014,  3032,  1032,  3031, 
2003,  2016,  4034,  2008,  4023,  253,  3002,  4002,  2002,  254, 
3018,  2014,  4014,  58,  2031,  4019,  3003,  252,  1023,  4026,  255, 
  3026,  1034,  1004,  1008,  2026,  4001,  1002,  2004,  2023,  1031, 
1001,  1026,  1018,  2001,  1003,  2034,  72, Total no of tracts: 664234 
connected tracts:5867811
Exception in thread "main" java.lang.IllegalArgumentException: ROI index 
out of bounds. This ROI contains 177 regions
         at tractography.FreeFormROI.getRegion(FreeFormROI.java:345)
         at apps.ConnectivityMapping.main(ConnectivityMapping.java:239)


At line 239 of ConnectivityMapping (FreeFormROI)allROIs.getRegion is 
called with the parameter 3007 which is greater than numberOfRegions 
which is 177, hence the error

Line 239
 > FreeFormROI fr = 
(FreeFormROI)allROIs.getRegion(roiIntensities.get(i)- 
allRoiIntensities.get(0));

When i = 0, roiIntensities.get(i) returns 3011, allRoiIntensities.get(0) 
returns 4

Is there a bug here or am I doing something wrong?


Many thanks

Gavin

P.S. The conmap wrapper has hard-coded paths unlike the other wrappers