Hi Francesco
yes, open tkmedit and load the existing control points, then add however many you want. You probably want to save the control.dat file before adding any though if you want to be able to go back to an older version
cheers Bruce
On Thu, 26 Sep 2013, Francesco Siciliano wrote:
Hi Bruce,
Sorry to persist, but I am not quite sure I understand what you mean. The main problem that I've been trying to resolve is that it appears to me that once you save a set of control points, that set can no longer be edited. So sometimes I either find an area that I neglected to put cps where they were needed, or as I mentioned previously, new problem areas arise during freeview editing. Because I cannot figure out a way to add cps to the previous cp set after it has been saved, short of beginning all over again, I have been creating additional .dat files named control2.dat, control3.dat, etc.
I now understand that recon-all is not configured to recognize files in the tmp folder this way. Is there a way that I can add to a previous control point set without beginning again, such that I can continue to add to one .dat file?
Thanks, Francesco ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 26, 2013 12:50 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] [FreeSurfer] multiple sets of control points
Hi Francesco
please cc the list so that others can answer! This isn't the way recon-all works, but I think you can achieve what you want by copying the control.dat to control.1.dat or some such before you add additional control points so you can always go back to a previous version
cheers Bruce
On Thu, 26 Sep 2013, Francesco Siciliano wrote:
Hi Bruce,
When I edit a brain a second and third time, it is helpful to create new control point files while maintaining the old ones. Because edits are not an exact science, I've noticed that sometimes new problems arise after a first edit. In my experience, creating a new control.dat file and overwriting the old one will undo the edits of the original set of control points (hence why it is useful to have multiple sets such that the original set remains in place and the second set can adjust new errors that have arisen). I understand what you mean - I try to place all of the control points I need in one sweep - however I cannot anticipate with certainty the combined effect of my edits, thus some situations call for multiple sets of control points on subsequent edits. Is it not possible to have multiple sets of control points recognized during a recon-all?
Thanks, Francesco ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 26, 2013 12:06 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu; Louis Nicholas Vinke Subject: Re: [Freesurfer] [FreeSurfer] multiple sets of control points
Hi Francesco
recon-all assumes that all the control points are in the single file <subject>/tmp/control.dat. Why are you separating them? Can you combine them?
cheers Bruce On Thu, 26 Sep 2013, Francesco Siciliano wrote:
Hello, I am currently having an issue getting my recon's to recognize multiple sets of control points. When I create a control point set, I make sure I select "control points", place them on the brainmask, and save them in the "tmp" folder as control.dat, control2.dat, control3.dat, etc.
I have been using the command recon-all -autorecon2 -autorecon3 -s Subject1
There does not seem to be a problem when I just have one set of control points. However, when I have multiple sets, I can see where control points have not been taken into account and have not altered the intensity of the voxels at all. I currently have them re-running with the command recon-all -autorecon2-cp -autorecon3 -s Subject1 to see if that makes a difference.
However, as I said before, one set of control points was previousy effective simply using the command recon-all -autorecon2 -autorecon3 -s Subject1
Any ideas?
Thanks, 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
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