for the aseg it's these lines: . . . pass 1: 89966 changed. image ll: -2.224, PF=1.000 pass 2: 15019 changed. image ll: -2.221, PF=1.000 pass 3: 5116 changed. pass 4: 2124 changed. writing labeled volume to aseg.auto_noCCseg.mgz...
although I guess I only compute it for the first couple of iterations of ICM
cheers Bruce
On Tue, 25 Jun 2013, Dov Sadan wrote:
This ?Computing Initial Surface Statistics -face loglikelihood: -8.0702 (-4.0351) -vertex loglikelihood: -6.6450 (-3.3225) -normal dot loglikelihood: -3.4961 (-3.4961) -quad curv loglikelihood: -6.1619 (-3.0810) Total Loglikelihood : -24.3732
On Tue, Jun 25, 2013 at 10:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: No, not that. That is the density reestimation. Later on it should write out the log posterior
On Jun 25, 2013, at 3:32 PM, Dov Sadan dov.sadan.19@gmail.com wrote:
Dear Buche,Thank you very much for your quick reply.
Do you mean those lines: (from recon-all. log)
. . . gca peak = 0.27536 (62) mri peak = 0.11940 (97) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, peak = 96), gca=96.1 . .
===================
If this is what you meant, can you shed some light on this log. What "gca peak" / "mri peak" means? And what the number insight the parentheses represent ?
Thanks in advance, Assaf
On Tue, Jun 25, 2013 at 9:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dov
I think it writes out the log posterior at each iteration of the aseg (mri_ca_label) cheers Bruce On Tue, 25 Jun 2013, Dov Sadan wrote: Hi there, I'm wondering if there's any parameter which can assess the correctness of the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file). --> Assuming the freesurfer's algorithm fitting/minimizing an objective function, right ? If so, where I can find the value of this fitted function ? (or RMS value ?) Thanks in advance, DovThe 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.
"LL" stand for *************************************L*og*L*ikelihood ? ;-)
On Tue, Jun 25, 2013 at 10:57 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
for the aseg it's these lines: . . . pass 1: 89966 changed. image ll: -2.224, PF=1.000 pass 2: 15019 changed. image ll: -2.221, PF=1.000 pass 3: 5116 changed. pass 4: 2124 changed. writing labeled volume to aseg.auto_noCCseg.mgz...
although I guess I only compute it for the first couple of iterations of ICM
cheers Bruce
On Tue, 25 Jun 2013, Dov Sadan wrote:
This ?Computing Initial Surface Statistics
-face loglikelihood: -8.0702 (-4.0351) -vertex loglikelihood: -6.6450 (-3.3225) -normal dot loglikelihood: -3.4961 (-3.4961) -quad curv loglikelihood: -6.1619 (-3.0810) Total Loglikelihood : -24.3732On Tue, Jun 25, 2013 at 10:34 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: No, not that. That is the density reestimation. Later on it should write out the log posterior
On Jun 25, 2013, at 3:32 PM, Dov Sadan dov.sadan.19@gmail.com wrote:
Dear Buche,Thank you very much for your quick reply.
Do you mean those lines: (from recon-all. log)
. . . gca peak = 0.27536 (62) mri peak = 0.11940 (97) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, peak = 96), gca=96.1 . .
===================
If this is what you meant, can you shed some light on this log. What "gca peak" / "mri peak" means? And what the number insight the parentheses represent ?
Thanks in advance, Assaf
On Tue, Jun 25, 2013 at 9:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dov
I think it writes out the log posterior at each iteration of the aseg (mri_ca_label) cheers Bruce On Tue, 25 Jun 2013, Dov Sadan wrote: Hi there, I'm wondering if there's any parameter which can assess the correctness of the freesurfer's segmentation **( the aparc.a2009s+aseg.mgz **file). --> Assuming the freesurfer's algorithm fitting/minimizing an objective function, right ? If so, where I can find the value of this fitted function ? (or RMS value ?) Thanks in advance, DovThe 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/**compliancelinehttp://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.
Yes, although I think it's actually the log posterior
On Jun 25, 2013, at 4:01 PM, Dov Sadan dov.sadan.19@gmail.com wrote:
"LL" stand for LogLikelihood ? ;-)
On Tue, Jun 25, 2013 at 10:57 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: for the aseg it's these lines: . . . pass 1: 89966 changed. image ll: -2.224, PF=1.000 pass 2: 15019 changed. image ll: -2.221, PF=1.000 pass 3: 5116 changed. pass 4: 2124 changed. writing labeled volume to aseg.auto_noCCseg.mgz...
although I guess I only compute it for the first couple of iterations of ICM
cheers Bruce
On Tue, 25 Jun 2013, Dov Sadan wrote:
This ?Computing Initial Surface Statistics
-face loglikelihood: -8.0702 (-4.0351) -vertex loglikelihood: -6.6450 (-3.3225) -normal dot loglikelihood: -3.4961 (-3.4961) -quad curv loglikelihood: -6.1619 (-3.0810) Total Loglikelihood : -24.3732On Tue, Jun 25, 2013 at 10:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: No, not that. That is the density reestimation. Later on it should write out the log posterior
On Jun 25, 2013, at 3:32 PM, Dov Sadan dov.sadan.19@gmail.com wrote:
Dear Buche,Thank you very much for your quick reply.
Do you mean those lines: (from recon-all. log)
. . . gca peak = 0.27536 (62) mri peak = 0.11940 (97) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (325 voxels, peak = 96), gca=96.1 . .
===================
If this is what you meant, can you shed some light on this log. What "gca peak" / "mri peak" means? And what the number insight the parentheses represent ?
Thanks in advance, Assaf
On Tue, Jun 25, 2013 at 9:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dov
I think it writes out the log posterior at each iteration of the aseg (mri_ca_label) cheers Bruce On Tue, 25 Jun 2013, Dov Sadan wrote: Hi there, I'm wondering if there's any parameter which can assess the correctness of the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file). --> Assuming the freesurfer's algorithm fitting/minimizing an objective function, right ? If so, where I can find the value of this fitted function ? (or RMS value ?) Thanks in advance, DovThe 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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Dov Sadan