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 utimesec 513.928000
mri_watershed stimesec 0.340000
mri_watershed ru_maxrss 370808
mri_watershed ru_ixrss 0
mri_watershed ru_idrss 0
mri_watershed ru_isrss 0
mri_watershed ru_minflt 172015
mri_watershed ru_majflt 0
mri_watershed ru_nswap 0
mri_watershed ru_inblock 0
mri_watershed ru_oublock 35688
mri_watershed ru_msgsnd 0
mri_watershed ru_msgrcv 0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw 4152
mri_watershed ru_nivcsw 5763
mri_watershed done
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
