External Email - Use Caution Hi! Just pinging. Is there a way to get the surface+overlay file as mentioned above using freesurfer? Thank you! Best regards, Sam
---------- Forwarded message --------- From: Sam W <samf...@gmail.com> Date: Fri, Jul 10, 2020 at 9:05 PM Subject: Re: [Freesurfer] label to surface To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Hi Doug and Tim, I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi). I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay. My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface. Best regards, Sam On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > what do you mean merge with the pial? > > On 7/9/2020 8:07 PM, Sam W wrote: > > External Email - Use Caution > It works great Doug, thanks a lot! > Can I ask you a follow up question please? I created the overlay with > mri_label2label using --outmask as you suggested, but now I'd like to merge > that overlay with the pial surface (lh.pial). Is there a tool I can use to > achieve that result? > Best regards, > Sam > > > On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> Use mri_label2label with the --outmask option >> >> On 7/8/2020 10:14 PM, Sam W wrote: >> >> External Email - Use Caution >> Hi, >> Is there a way to convert a label file into a surface/overlay? Thank you! >> Best regards, >> Sam >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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