Re: [Freesurfer] How to get deformation maps in surface-based registrations
I don't have it either. Regards, Thomas On May 18, 2010, at 4:51 PM, Bruce Fischl wrote: > I don't think we have anything to create the deformation field > explicitly, unless Thomas Yeo (ccd) does. > > cheers > Bruce > > On Tue, 18 May 2010, Xiaojing Long wrote: > >> Hi, Bruce, >> >> Thanks a lot for replying me. >> >> Do I have to create the deformation file by myself? Or can it be >> generated >> from >> some option set in mris_register? >> >> Thanks again. >> >> Best, >> >> Xiaojing >> >> >> >> >> 2010/5/18 Bruce Fischl >> >>> Hi Xiaojing, >>> >>> the deformation map is the difference between the ?h.sphere.reg >>> and the >>> ?h.sphere. I guess you would want to represent them as arcs of great >>> circles. >>> >>> cheers, >>> Bruce >>> >>> On Tue, 18 May 2010, Xiaojing Long wrote: >>> >>> Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing >>> >>> 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
Re: [Freesurfer] tksurfer tcl scripting: Environment variables for hemisphere and subject
There's a tksurfer scripting reference here: http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference --Thomas On May 21, 2010, at 9:39 AM, Bruce Fischl wrote: > probably, but I don't know what it is. You can look in tksurfer.tcl to > see if you can find it. > > cheers > Bruce > On Fri, 21 May 2010, Andreas Schindler wrote: > >> Thanks! :-) >> >> btw: Is there a tcl interface for View -> Configure -> Phase Encoded >> Data Display: Angle Cycles ? >> >> bw >> >> Andreas >> >> >> >> Bruce Fischl wrote: >>> Hi Andreas, >>> >>> the tcl variables $subject and $hemi should be set properly by >>> tksurfer, so >>> you can use them generically. >>> >>> cheers >>> Bruce >>> >>> On Fri, 21 May 2010, Andreas Schindler wrote: >>> >>> Hello I am currently writing a tcl script for tksurfer which I am using for several subjects. That's why I am wondering if it is possible to avoid adapting this tcl script for every subject by reading out tksurfer's variables for hemisphere and subject as they are committed by the shell, anyway. Many thanks bw Andreas ___ 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 >>> >>> >>> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Having Matlab portion run as compiled matlab
Hi Bill, you want to look at mcc (http://www.mathworks.com/help/toolbox/compiler/mcc.html ) Usually what works for me is something like: mcc -m -v matlab_file.m This will generate a console executable "matlab_file" --Thomas On Jul 19, 2011, at 3:02 PM, Bill Taylor wrote: > So I peaked in archive and did not get a hit. > > The situation is that the University of Wisconsin > Madison site license prohibits us running Matlab > in a cluster unless it is compiled. > > I am assisting a Neurology lab with having a Condor > workflow which this time round will do both Matlab > and FSL post processing. > > To compile the Matlab one needs to compile the > entry points. But to run it, we'd have to change how it is called. > > Anyone have pointers for me? > > Bill Taylor > Center for High Throughput Computing > Condor Project > Computer Sciences > University of Wisconsin, Madison > 608-219-4430 > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
