Hi, I would like to translate a label created from an average subject inflated surface to all the subjects. How would I do that? Should I first use mri_surf2surf to resample the average subject inflated surface to all the other subjects? Would a label that was created on the average subject then automatically be translatable to the subjects?
Thanks, Jon
Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel
Ooops. I sent the below with the wrong subject tag. Here it is again:
Daniel Goldenholz wrote:
Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel
The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible.
On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote:
Ooops. I sent the below with the wrong subject tag. Here it is again:
Daniel Goldenholz wrote:
Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel
Nick
I completely agree with you. However, I didn't want to edit recon-all itself, since it has this funny tendency to change from time to time. If there is a way to get those logs separated somehow, it would be a good thing. What about redirecting stdout to a hemisphere specific file? Will that cover everything?
D
Nick Schmansky wrote:
The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible.
On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote:
Ooops. I sent the below with the wrong subject tag. Here it is again:
Daniel Goldenholz wrote:
Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel
Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick. I have now included those into my super-recon script as well. Problem solved.
(if you have seen my script already, you may need to hit RELOAD on your browser to see the new version) Daniel
Nick Schmansky wrote:
The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible.
On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote:
Ooops. I sent the below with the wrong subject tag. Here it is again:
Daniel Goldenholz wrote:
Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel
Hi Jon,
You should use mri_label2label.
mri_label2label --help will give you usage and examples.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Jonathan Wisco Sent: Wednesday, March 15, 2006 5:50 PM To: Freesurfer Subject: [Freesurfer] Translate label file from average subject to allsubjects
Hi, I would like to translate a label created from an average subject inflated surface to all the subjects. How would I do that? Should I first use mri_surf2surf to resample the average subject inflated surface to all the other subjects? Would a label that was created on the average subject then automatically be translatable to the subjects?
Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco@nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422
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