Hi,
I am having a problem with mri_watershed. The data is @ /space/linus/12/users/dwakeman/subjects/P1B2au1/ I called recon-all -subjid P1B2au1 -autorecon1 The error message is at the bottom. running mri_watershed -atlas T1.mgz brain did not work. There is no brain.mgz file generated, so I cannot look to see what the problem is.
I have one other problem on a side note, I am generating a true step by step tutorial, which will serve to both teach people about freesurfer and teach them how to use it. I am using the Recommended ReconTable as a basis for this tutorial. In the table, it says that autorecon1 does 4 iterations of nu_correct; however, when the nu_correct command is run individually it says that it performs 2 iterations. I would like to know if this means that a total of 8 iterations are run in autorecon1 or if the equivalent to autorecon1 is two iterations of the nu_correct command.
Thank you for your help on both problems. Dan
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 253666
Find the largest 110-component... heap usage = 243888 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 243349 voxels first estimation of the COG coord: x=128 y=128 z=120 r=87 first estimation of the main basin volume: 2802165 voxels global maximum in x=144, y=108, z=79, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 done Analyze
main basin size= 1769198 voxels, voxel volume =1.000 = 1769198 mmm3 = 1769.198 cm3 done PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done
****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=134, z=118, r=10259 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=45, TRANSITION=40, GM_MIN=37, GM=52 after analyzing : CSF_MAX=35, TRANSITION=40, GM_MIN=40, GM=43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations
*********************VALIDATION*********************Segmentation fault ERROR: mri_watershed exited with non-zero status Linux megws2 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux recon-all exited with errors at Wed Jan 11 17:07:18 EST 2006
Hi Dan,
the watershed core dump is a known bug that I think will be fixed in tomorrow's dev version (not positive though).
Looking at recon-all I think it runs it without any # of iterations on the command. Not sure what the default is for it in terms of # of iters.
cheers, Bruce
On Wed, 11 Jan 2006 dwakeman@nmr.mgh.harvard.edu wrote:
Hi,
I am having a problem with mri_watershed. The data is @ /space/linus/12/users/dwakeman/subjects/P1B2au1/ I called recon-all -subjid P1B2au1 -autorecon1 The error message is at the bottom. running mri_watershed -atlas T1.mgz brain did not work. There is no brain.mgz file generated, so I cannot look to see what the problem is.
I have one other problem on a side note, I am generating a true step by step tutorial, which will serve to both teach people about freesurfer and teach them how to use it. I am using the Recommended ReconTable as a basis for this tutorial. In the table, it says that autorecon1 does 4 iterations of nu_correct; however, when the nu_correct command is run individually it says that it performs 2 iterations. I would like to know if this means that a total of 8 iterations are run in autorecon1 or if the equivalent to autorecon1 is two iterations of the nu_correct command.
Thank you for your help on both problems. Dan
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 253666
Find the largest 110-component... heap usage = 243888 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 243349 voxels first estimation of the COG coord: x=128 y=128 z=120 r=87 first estimation of the main basin volume: 2802165 voxels global maximum in x=144, y=108, z=79, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110done Analyze
main basin size= 1769198 voxels, voxel volume =1.000 = 1769198 mmm3 = 1769.198 cm3done PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done
****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=134, z=118, r=10259 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=45, TRANSITION=40, GM_MIN=37, GM=52 after analyzing : CSF_MAX=35, TRANSITION=40, GM_MIN=40, GM=43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations
*********************VALIDATION*********************Segmentation fault ERROR: mri_watershed exited with non-zero status Linux megws2 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux recon-all exited with errors at Wed Jan 11 17:07:18 EST 2006
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