Hi Daniel, The script is ok but it still does not make it to the end. As the script is designed to send me an email at the end of the last step, I got an email within 15 min after I executed the script saying that "recon-all 14777 finished with errors at Tue Mar 21 18:46:15 EST 2006". However it went on the complete the "gcareg" step. I have attached the status and log files for your reference. If you get a chance have a look at it. I believe this problem is not due to super-recon script but due to recon-all script. Please let me know. I am very interested in the super-recon script, as it takes about 30 hrs to process 1 scan currently. -Dhruman
-----Original Message----- From: Daniel Goldenholz [mailto:daniel@nmr.mgh.harvard.edu] Sent: Tuesday 21 March 2006 17:09 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faster and Parallel recon-all
Dhruman
Thanks for catching that. Spelling was never my strong point. I have corrected the script on my website.
As for you second problem, did you properly remove the waitfor step1-00.done from the motion correction step, since you say you skipped step1-00, i.e. the invol step? I mention this in a comment near the top of the script.
D
Goradia, Dhruman D wrote:
Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in "scripts" where "t" is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman
-----Original Message----- From: Daniel Goldenholz [mailto:danielg@bu.edu] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all
Dhruman
That's confusing. I think you should take one line of executable code from your script that produces that behavior and then email it to the freesurfer list.
It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a
few
extra lines of code. PLEASE follow up on this. It will help others.
The other thing to try is to create a text file first, such as like this: echo "#Starting recon-all manually..." > /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log
and then see if my script is ok.
Keep me posted.
D
Goradia, Dhruman D wrote:
Hi Daniel, I tried to use the script super-recon on mac OX S using bash shell. I made the necessary changes to make it operable in bash. However when I run the script its gives me the following error:
Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.l
o
g
:not a file or directory.
I tried to run the first 3 steps of the script (motioncor, nuintensitycor, talairach) and it gives the above error. However if I remove the log and status flags, the first 3 steps executes properly.
Do
you have any idea why? Do you see any problem if I delete the log and status flags from the whole script and use it? -Dhruman
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel Goldenholz Sent: Thursday 16 March 2006 15:17 Cc: Freesurfer Mailing List; Nick Schmansky Subject: Re: [Freesurfer] Faster and Parallel recon-all
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again,
I have totally revamped the script in light of the fact that recon-all -notify did not do what I thought it did at all! The new and improved (version 1.02) super-recon is quite a bit fancier. Now, I leave all notifcations and waiting and emailing to super-recon itself, so that recon-all assumptions are reduced.
If you want to run a complete recon-all -all but have the hemisphere parts run in parallel, you run a command like this one: super_recon all $SUBJECTS_DIR $SUBJECT /space/dicom/file1 /space/dicom/file2 my_email@wherever.nmr.com
Using this new and improved command, if you have a cluster with daul processors, then you should be able to run multiple subjects faster than a standard recon-all command.
The script in "all" mode will run the same stuff as recon-all -all. If you wish to run a subset of the full set of commands, you can simply comment out a specific line you don't want. There are also several other ways to call the script now, since in reality it calls itself recursively with different options.
Hopefully this one will do what the original one intended to do. Good luck, Daniel
Goradia, Dhruman D wrote:
Hi Daniel, The script is ok but it still does not make it to the end. As the script is designed to send me an email at the end of the last step, I got an email within 15 min after I executed the script saying that "recon-all 14777 finished with errors at Tue Mar 21 18:46:15 EST 2006". However it went on the complete the "gcareg" step. I have attached the status and log files for your reference. If you get a chance have a look at it. I believe this problem is not due to super-recon script but due to recon-all script. Please let me know. I am very interested in the super-recon script, as it takes about 30 hrs to process 1 scan currently. -Dhruman
-----Original Message----- From: Daniel Goldenholz [mailto:daniel@nmr.mgh.harvard.edu] Sent: Tuesday 21 March 2006 17:09 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faster and Parallel recon-all
Dhruman
Thanks for catching that. Spelling was never my strong point. I have corrected the script on my website.
As for you second problem, did you properly remove the waitfor step1-00.done from the motion correction step, since you say you skipped step1-00, i.e. the invol step? I mention this in a comment near the top of the script.
D
Goradia, Dhruman D wrote:
Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in "scripts" where "t" is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman
-----Original Message----- From: Daniel Goldenholz [mailto:danielg@bu.edu] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all
Dhruman
That's confusing. I think you should take one line of executable code
from your script that produces that behavior and then email it to the
freesurfer list.
It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a
few
extra lines of code. PLEASE follow up on this. It will help others.
The other thing to try is to create a text file first, such as like this: echo "#Starting recon-all manually..." > /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log
and then see if my script is ok.
Keep me posted.
D
Goradia, Dhruman D wrote:
Hi Daniel, I tried to use the script super-recon on mac OX S using bash shell. I made the necessary changes to make it operable in bash. However when I run the script its gives me the following error:
Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.l
o
g
:not a file or directory.
I tried to run the first 3 steps of the script (motioncor, nuintensitycor, talairach) and it gives the above error. However if I remove the log and status flags, the first 3 steps executes properly.
Do
you have any idea why? Do you see any problem if I delete the log and status flags from the whole script and use it? -Dhruman
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Daniel Goldenholz Sent: Thursday 16 March 2006 15:17 Cc: Freesurfer Mailing List; Nick Schmansky Subject: Re: [Freesurfer] Faster and Parallel recon-all
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 > > > > > > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Daniel Goldenholz -
Goradia, Dhruman D