Hi:
I got the following error... How can I solve it ?...
recon-all.log ----------------------------------------------------------------- mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details)
********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C
Weighting the input with atlas information before watershed
*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=122 z=99 r=84 first estimation of the main basin volume: 2562881 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=120, z=70, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze
main basin size=33359051 voxels, voxel volume =1.000 = 33359051 mmm3 = 33359.051 cm3 done PostAnalyze...Basin Prior 86 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=125, z=105, r=9959 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 22212 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1368 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1242 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 9603 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=49 , nb = 9792 OTHER CSF_MIN=0, CSF_intensity=33, CSF_MAX=47 , nb = 207 mri_watershed Error: GLOBAL region of the brain empty ! Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009
check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n.
On Wed, 2009-10-07 at 15:34 -0400, Gonzalo Rojas wrote:
Hi:
I got the following error... How can I solve it ?...
recon-all.log
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details)
The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C
Weighting the input with atlas information before watershed
*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=122 z=99 r=84 first estimation of the main basin volume: 2562881 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=120, z=70, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze
main basin size=33359051 voxels, voxel volume =1.000 = 33359051 mmm3 = 33359.051 cm3done PostAnalyze...Basin Prior 86 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=125, z=105, r=9959iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 22212 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1368 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1242 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 9603 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=49 , nb = 9792 OTHER CSF_MIN=0, CSF_intensity=33, CSF_MAX=47 , nb = 207 mri_watershed Error: GLOBAL region of the brain empty ! Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009
Hi:
Yes... the occipital white matter has value 110 in general... The frontal white matter has voxels with values 94 to 117 aprox...
Sincerely,
Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Nick Schmansky escribió:
check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n.
another thing to try is include the flag -no-wsgcaatlas flag, like this:
recon-all -s subjid -skull-strip -no-wsgcaatlas
this bypasses usage of the atlas.
if that fails, you can send me the 001.mgz input file to the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
n.
On Wed, 2009-10-07 at 16:48 -0400, Gonzalo Rojas wrote:
Hi:
Yes... the occipital white matter has value 110 in general... The frontal white matter has voxels with values 94 to 117 aprox...
Sincerely,
Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Nick Schmansky escribió:
check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n.
Hi:
Ok... I test it with the command that you told me, and I added the option "wsthresh 35"... Then I got a good skull stripped image...
Sincerely,
Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Nick Schmansky escribió:
another thing to try is include the flag -no-wsgcaatlas flag, like this:
recon-all -s subjid -skull-strip -no-wsgcaatlas
this bypasses usage of the atlas.
if that fails, you can send me the 001.mgz input file to the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
n.
Hi:
How can I put the control points in the nu.mgz image ?...
Sincerely
Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Nick Schmansky escribió:
check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n.
sorry, it doesn't sound like this is the problem. You could try putting some seed points in the white matter for the watershed. Not sure what the interface is for that. You should also check to make sure that the atlas transform it is using is reasonable.
On Wed, 7 Oct 2009, Gonzalo Rojas wrote:
Hi:
How can I put the control points in the nu.mgz image ?...
Sincerely
Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Nick Schmansky escribió:
check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
check to see if the intensity normalization worked (does the T1.mgz white matter have intensities of 110 most places) On Wed, 7 Oct 2009, Gonzalo Rojas wrote:
Hi:
I got the following error... How can I solve it ?...
recon-all.log
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details)
The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C
Weighting the input with atlas information before watershed
*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=122 z=99 r=84 first estimation of the main basin volume: 2562881 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=120, z=70, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze
main basin size=33359051 voxels, voxel volume =1.000 = 33359051 mmm3 = 33359.051 cm3done PostAnalyze...Basin Prior 86 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=125, z=105, r=9959iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 22212 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1368 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1242 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 9603 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=49 , nb = 9792 OTHER CSF_MIN=0, CSF_intensity=33, CSF_MAX=47 , nb = 207 mri_watershed Error: GLOBAL region of the brain empty ! Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Gonzalo Rojas -
Nick Schmansky