Re: [Freesurfer] mri_watershed seed point

2017-04-05 Thread Antonin Skoch 
Dear Kristen,

looking at the source code of mri_watershed, the seed point has to be specified 
in the format:
-s i j k

and the option can be specified more than once when you want to add more seed 
points (30 seed points is maximum).

i.e., when you want to input seed points in coordinates 50,60,70, and 
80,90,100, the option would be:
-s 50 60 70 -s 80 90 100

Regards,

Antonin Skoch



Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] 
./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen___
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[Freesurfer] mri_watershed seed point

2017-04-05 Thread Kanoff, Kristen Elise 
Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:

mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen


Kristen Kanoff
Clinical Research Coordinator II
Department of Neurology
Massachusetts General Hospital
Boston, MA
Ph: 617-726-3958
osboxes@osboxes:~/Documents/freesurfer/subjects/iDBS002/mri$ mri_watershed 
-atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol

Mode:  Atlas analysis
Mode:  use surfaceRAS to save surface vertex positions
Mode:  Saving out BEM surfaces

*
The input file is ./T1.mgz
The output file is ./brainvol

*WATERSHED**
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  176432

  Find the largest 110-component...
 heap usage = 336340 Kbytes.
 current max segment has 154566 voxels
 removing small segments (less than 1 percent of maxarea).
 heap usage = 130864 Kbytes.
 removing small segments (less than 1 percent of maxarea).done
  And identify it as the main brain basin...done
  Main component: 154566 voxels
  first estimation of the COG coord: x=128 y=122 z=94 r=81
  first estimation of the main basin volume: 2241917 voxels
  global maximum in x=146, y=114, z=55, Imax=255
  CSF=24, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
  preflooding height equal to 15 percent
done.
Analyze...

  main basin size=34171332 voxels, voxel volume =1.000 
 = 34171332 mmm3 = 34171.332 cm3
done.
PostAnalyze...
  ambiguous basin, merged: at least 12 ambiguous voxels; size: 1490 voxels
  ambiguous basin, merged: at least 4 ambiguous voxels; size: 60 voxels
  ambiguous basin, merged: at least 11 ambiguous voxels; size: 1280 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 260 voxels
  ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 307 voxels
  * 6 basin(s) merged in 4 iteration(s)
  * 4310 voxel(s) added to the main basin
  ambiguous basin, non merged: 6 ambiguous voxels; size: 2335 voxels
done.

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=120, z=92, r=12891 iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 43064
 Problem with the least square interpolation in GM_MIN calculation.
   
 CSF_MAX  TRANSITION  GM_MIN  GM
GLOBAL 
  before analyzing :31,  29,28,   54
  after  analyzing :20,  29,29,   35
  mri_strip_skull: done peeling brain
  highly tesselated surface with 10242 vertices
  matching...59 iterations

*VALIDATION*
curvature mean = -0.013, std = 0.011
curvature mean = 67.196, std = 9.490

Rigid alignment...
  scanning 32.00 degree nbhd, min sse =  6.39 at ( 0.00,  8.00,  8.00)
  scanning 16.00 degree nbhd, min sse =  6.10 at ( 0.00, -4.00, -4.00)
  scanning  8.00 degree nbhd, min sse =  6.10 at ( 0.00,  0.00,  0.00)
  scanning  4.00 degree nbhd, min sse =  6.08 at ( 1.00,  1.00,  1.00)
done
  before rotation: sse = 6.68, sigma = 13.72
  after  rotation: sse = 6.08, sigma = 10.80
Localization of inacurate regions: Erosion-Dilation steps
  the sse mean is  7.43, its var is 10.75   
  before Erosion-Dilatation  6.23% of inacurate vertices
  after  Erosion-Dilatation  9.18% of inacurate vertices
  Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

FINAL ITERATIVE TEMPLATE DEFORMATION
Compute Local values csf/gray
Fine Segmentation...40 iterations

  mri_strip_skull: done peeling brain

Brain Size = 1413043 voxels, voxel volume = 1.000 mm3
   = 1413043 mmm3 = 1413.043 cm3

  outer skin surface matching...187 iterations

**
Saving ./brainvol
done
mri_watershed utimesec513.928000
mri_watershed