Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari
There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga garikoitz@gmail.com wrote:
Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ender asked me to forward you this:
I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal.
An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga garikoitz@gmail.com wrote:
Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks!
I can visualize the 3D renders of interest with different colors, but from "freeview -h" I couldn't get the following: is it possible to automatize the "File > Save movie frames" option?
Thanks again! Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Ender asked me to forward you this:
I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal.
An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run 'freeview
-h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
garikoitz@gmail.com> wrote:
Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Sure.
I couldn't find that option neither.
What I did was to semi-automatize. I wrote a batch file to call freeview multiple times with different parameters. Each time freeview pops up and I save the image/video. During this time the process in the terminal waits for me. When I shut that window the next freeview window pops up and I do the same.
Ender
On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
Thanks!
I can visualize the 3D renders of interest with different colors, but from "freeview -h" I couldn't get the following: is it possible to automatize the "File > Save movie frames" option?
Thanks again! Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu mailto:iglesias@nmr.mgh.harvard.edu> wrote:
Ender asked me to forward you this: I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal. An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180 Let me know if this helps. Cheers, E On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote: > There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options. > > Ruopeng > > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com <mailto:garikoitz@gmail.com>> wrote: > > > Hi list, > > is it possible to automate Freeview automation from the command line? > > > > I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking. > > > > thanks! > > Gari > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Ender, I am trying to make a command file with multiple commands too in order to have snapshots from different views.
thanks for the help! Gari
On Fri, May 31, 2013 at 5:13 PM, Ender Konukoglu <enderk@nmr.mgh.harvard.edu
wrote:
Sure.
I couldn't find that option neither.
What I did was to semi-automatize. I wrote a batch file to call freeview multiple times with different parameters. Each time freeview pops up and I save the image/video. During this time the process in the terminal waits for me. When I shut that window the next freeview window pops up and I do the same.
Ender
On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
Thanks!
I can visualize the 3D renders of interest with different colors, but from "freeview -h" I couldn't get the following: is it possible to automatize the "File > Save movie frames" option?
Thanks again! Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Ender asked me to forward you this:
I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal.
An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run 'freeview
-h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
garikoitz@gmail.com> wrote:
Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
If you use '-ss' option, freeview will save a screenshot and close itself. For example:
freeview -v foo.mgz -ss foo.jpg
On 05/31/2013 11:13 AM, Ender Konukoglu wrote:
Sure.
I couldn't find that option neither.
What I did was to semi-automatize. I wrote a batch file to call freeview multiple times with different parameters. Each time freeview pops up and I save the image/video. During this time the process in the terminal waits for me. When I shut that window the next freeview window pops up and I do the same.
Ender
On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
Thanks!
I can visualize the 3D renders of interest with different colors, but from "freeview -h" I couldn't get the following: is it possible to automatize the "File > Save movie frames" option?
Thanks again! Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <iglesias@nmr.mgh.harvard.edu mailto:iglesias@nmr.mgh.harvard.edu> wrote:
Ender asked me to forward you this: I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal. An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180 Let me know if this helps. Cheers, E On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote: > There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options. > > Ruopeng > > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com <mailto:garikoitz@gmail.com>> wrote: > > > Hi list, > > is it possible to automate Freeview automation from the command line? > > > > I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking. > > > > thanks! > > Gari > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks! it is working perfectly, I created a command file to take several screenshots, for example:
[...] -cam azimuth 90 -ss imagen6.png -cam azimuth 90 -cam Elevation 90 -ss imagen7.png -slice 127 180 127 -ss imagen8.png -slice 127 80 127 -cam Elevation 180 -ss imagen9.png -quit
On Fri, May 31, 2013 at 5:34 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.eduwrote:
If you use '-ss' option, freeview will save a screenshot and close itself. For example:
freeview -v foo.mgz -ss foo.jpg
On 05/31/2013 11:13 AM, Ender Konukoglu wrote:
Sure.
I couldn't find that option neither.
What I did was to semi-automatize. I wrote a batch file to call freeview multiple times with different parameters. Each time freeview pops up and I save the image/video. During this time the process in the terminal waits for me. When I shut that window the next freeview window pops up and I do the same.
Ender
On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
Thanks!
I can visualize the 3D renders of interest with different colors, but from "freeview -h" I couldn't get the following: is it possible to automatize the "File > Save movie frames" option?
Thanks again! Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Ender asked me to forward you this:
I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal.
An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
Let me know if this helps.
Cheers,
E
On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
There is a screenshot option -ss from the command-line. Run 'freeview
-h' will show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
garikoitz@gmail.com> wrote:
Hi list, is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all subjects for quality checking.
thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Ender Konukoglu -
Garikoitz Lerma-Usabiaga -
Juan Eugenio Iglesias -
Ruopeng Wang