Hello,
I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue?
-Francesco
Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155
Hi Francesco
where do you save the file control.dat? It must be in the directory $SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers Bruce
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hello, I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue?
-Francesco
Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155
Hi Bruce,
Yes, I save it in the subject's tmp folder.
-Francesco ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 12:47 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] control points
Hi Francesco
where do you save the file control.dat? It must be in the directory $SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers Bruce
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hello, I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue?
-Francesco
Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155
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 many control points are in it? Can you check the recon-all.log to see if it says it reads as many as you think you should have (in the mri_normalize step)? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hi Bruce,
Yes, I save it in the subject's tmp folder.
-Francesco ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 12:47 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] control points
Hi Francesco
where do you save the file control.dat? It must be in the directory $SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers Bruce
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hello, I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue?
-Francesco
Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155
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.
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
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Francesco Siciliano