Thank you for your help!
I will re-run this brain and see if it reads all 53 control points and then let you know the outcome. However, the last time I ran this brain with this control point set, it only read 22 control points. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:28 PM To: Francesco Siciliano Subject: RE: brain.mgz and control.dat attached
but it should say "reading 53 control points". Can you verify whether this is or is not the case? And also please cc the list so that others can answer! On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I can run it again - but it has already been run with the current control point set (apparently with 53 points) and some of the points have not been successful for some reason. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:55 PM To: Francesco Siciliano Subject: Re: brain.mgz and control.dat attached
hmmm, and you reran after this? There are 53 points in it. Can you run autorecon2-cp and see if it now reads 53 control points? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:48 PM To: Francesco Siciliano Subject: RE: [Freesurfer] [FreeSurfer] control points
can you email me the control.dat and the brain.mgz?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
In the control.dat file it says numpoints 53. Is that referring to control points? Because I certainly don't have that many! I counted about 28 when I loaded the control.dat file onto the brainmask volume. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:14 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] [FreeSurfer] control points
and how many do you see in the control.dat file? Sounds like they aren't getting saved to disk somehow.... On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I counted at least 28 control points on the brainmask when I loaded the set and my log indicates that freesurfer read 22 control points. I've attached part of the log below.
#@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013 /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/mri \n mri_normalize -f /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n using control points from file /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 22 control points... only using 22 control points from file, mean 84.1, scaling by 1.31... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 4899 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 46 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 102 gm peak at 66 (66), valley at 25 (25) csf peak at 33, setting threshold to 55 white matter peak found at 111 white matter peak found at 110 gm peak at 66 (66), valley at 24 (24) csf peak at 33, setting threshold to 55
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My recon-all log says that 53 control points were read. However, the same control points still have not taken effect. Earlier in the log, it says 22 control points were read. I have attached my log for you to look at.
Thanks, Francesco ________________________________________ From: Francesco Siciliano Sent: Monday, October 07, 2013 3:42 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: brain.mgz and control.dat attached
Thank you for your help!
I will re-run this brain and see if it reads all 53 control points and then let you know the outcome. However, the last time I ran this brain with this control point set, it only read 22 control points. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:28 PM To: Francesco Siciliano Subject: RE: brain.mgz and control.dat attached
but it should say "reading 53 control points". Can you verify whether this is or is not the case? And also please cc the list so that others can answer! On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I can run it again - but it has already been run with the current control point set (apparently with 53 points) and some of the points have not been successful for some reason. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:55 PM To: Francesco Siciliano Subject: Re: brain.mgz and control.dat attached
hmmm, and you reran after this? There are 53 points in it. Can you run autorecon2-cp and see if it now reads 53 control points? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:48 PM To: Francesco Siciliano Subject: RE: [Freesurfer] [FreeSurfer] control points
can you email me the control.dat and the brain.mgz?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
In the control.dat file it says numpoints 53. Is that referring to control points? Because I certainly don't have that many! I counted about 28 when I loaded the control.dat file onto the brainmask volume. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:14 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] [FreeSurfer] control points
and how many do you see in the control.dat file? Sounds like they aren't getting saved to disk somehow.... On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I counted at least 28 control points on the brainmask when I loaded the set and my log indicates that freesurfer read 22 control points. I've attached part of the log below.
#@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013 /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/mri \n mri_normalize -f /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n using control points from file /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 22 control points... only using 22 control points from file, mean 84.1, scaling by 1.31... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 4899 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 46 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 102 gm peak at 66 (66), valley at 25 (25) csf peak at 33, setting threshold to 55 white matter peak found at 111 white matter peak found at 110 gm peak at 66 (66), valley at 24 (24) csf peak at 33, setting threshold to 55
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.
how do you know that they have not taken effect? The log is cumulative, so if you ran once with 23 then added more that's what you would see
On Tue, 8 Oct 2013, Francesco Siciliano wrote:
My recon-all log says that 53 control points were read. However, the same control points still have not taken effect. Earlier in the log, it says 22 control points were read. I have attached my log for you to look at.
Thanks, Francesco ________________________________________ From: Francesco Siciliano Sent: Monday, October 07, 2013 3:42 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: brain.mgz and control.dat attached
Thank you for your help!
I will re-run this brain and see if it reads all 53 control points and then let you know the outcome. However, the last time I ran this brain with this control point set, it only read 22 control points. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:28 PM To: Francesco Siciliano Subject: RE: brain.mgz and control.dat attached
but it should say "reading 53 control points". Can you verify whether this is or is not the case? And also please cc the list so that others can answer! On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I can run it again - but it has already been run with the current control point set (apparently with 53 points) and some of the points have not been successful for some reason. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:55 PM To: Francesco Siciliano Subject: Re: brain.mgz and control.dat attached
hmmm, and you reran after this? There are 53 points in it. Can you run autorecon2-cp and see if it now reads 53 control points? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:48 PM To: Francesco Siciliano Subject: RE: [Freesurfer] [FreeSurfer] control points
can you email me the control.dat and the brain.mgz?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
In the control.dat file it says numpoints 53. Is that referring to control points? Because I certainly don't have that many! I counted about 28 when I loaded the control.dat file onto the brainmask volume. ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 2:14 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] [FreeSurfer] control points
and how many do you see in the control.dat file? Sounds like they aren't getting saved to disk somehow.... On Mon, 7 Oct 2013, Francesco Siciliano wrote:
I counted at least 28 control points on the brainmask when I loaded the set and my log indicates that freesurfer read 22 control points. I've attached part of the log below.
#@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013 /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/mri \n mri_normalize -f /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n using control points from file /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 22 control points... only using 22 control points from file, mean 84.1, scaling by 1.31... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 4899 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 46 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 102 gm peak at 66 (66), valley at 25 (25) csf peak at 33, setting threshold to 55 white matter peak found at 111 white matter peak found at 110 gm peak at 66 (66), valley at 24 (24) csf peak at 33, setting threshold to 55
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Francesco Siciliano