Hi James, Freeview has a "Write Movie Frames" option which will grab multiple screenshots throughout a volume. I recently requested a commandline option for this. I've run into the "no X11 on cluster" limitation as well, and I don't have a work-around at this point.

The snapshot-to-html script is roughly implemented in the set of QATools scripts using tkmedit. I have an alternate version which gets snaps with freeview, but it runs faster with tkmedit at this point. https://surfer.nmr.mgh.harvard.edu/fswiki/QATools -Louis

On Mon, 23 Jun 2014, Bruce Fischl wrote:

Hi James

Ruopeng is traveling and may not answer quickly, although Louis might be able to help Bruce On Mon, 23 Jun 2014, james pardon wrote:

...

Sorry if you are receiving this for the second time , not really sure if this went through the first time I sent the email:

Dear all,  I'm looking for a way to automate surface on volume visualization, to check if the surface reconstruction have been successful on a very large number of subjects. Normally, I would use freeview with -f and -v flags to check and see if it is necessary to edit controls points, etc.

As an example, one option to automate this process is to use freeview snapshot option and write a script that runs on several hundred subjects and then show all the resulting images in html format.  Running freeview with snapshot option works really good, however, since every freeview run needs X11 there is an overhead here, especially when I'm running on a remote cluster with no X11, which makes running X11 almost impossible.

I'm wondering whether any one has a better idea for this?

Thanks James

Hi James, It's not possible (currently?) to get snapshots with Freeview or the tktools without invoking X. I can post a link for the modified script which uses Freeview instead of the tktools. It's much slower though and until the movie frame capture is a commandline option, using the tktools is probably best.

Just stumbled upon xvfb which might do the trick. http://en.wikipedia.org/wiki/Xvfb

-Louis

On Wed, 2 Jul 2014, james pardon wrote:

Dear Louis, Thank you for your comprehensive response, the QA tools are certainly valuable tools. I'm very curious on how I could go about getting Freeview snapshots without invoking X. I was wondering whether you are happy to share your "alternative version which gets snaps with freeview"? Or perhaps more generally, how a programmer should approach this problem of not invoking X when getting the snapshot?

Thanks James

On Tue, Jul 1, 2014 at 10:30 PM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: Hi James, Freeview has a "Write Movie Frames" option which will grab multiple screenshots throughout a volume.  I recently requested a commandline option for this.  I've run into the "no X11 on cluster" limitation as well, and I don't have a work-around at this point.

  The snapshot-to-html script is roughly implemented in the set of QATools scripts using tkmedit.  I
  have an alternate version which gets snaps with freeview, but it runs faster with tkmedit at this
  point.
  https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
  -Louis

  On Mon, 23 Jun 2014, Bruce Fischl wrote:

        Hi James

        Ruopeng is traveling and may not answer quickly, although Louis might be able to help
        Bruce
        On Mon, 23 Jun 2014, james pardon wrote:

              Sorry if you are receiving this for the second time , not really sure if
              this went through the first time I sent the email:


              Dear all, 
              I'm looking for a way to automate surface on volume visualization, to check
              if the surface reconstruction have been successful on a very large number
              of
              subjects. Normally, I would use freeview with -f and -v flags to check and
              see if it is necessary to edit controls points, etc. 

              As an example, one option to automate this process is to use freeview
              snapshot option and write a script that runs on several hundred subjects
              and
              then show all the resulting images in html format.  Running freeview with
              snapshot option works really good, however, since every freeview run needs
              X11 there is an overhead here, especially when I'm running on a remote
              cluster with no X11, which makes running X11 almost impossible. 

              I'm wondering whether any one has a better idea for this? 

              Thanks
              James

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