thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote:
Hi Bruce,
Connectome Workbench commandline utilities can do this with FSL warp fields:
wb_command -surface-apply-warpfield
One needs to use the inverse warp as the <warpfield> argument and the forward warp as the -fnirt <forward-warp>.
Peace,
Matt.
On 9/2/13 11:19 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
A veritable game of telephone! Thanks Jesper. Matt?
On Mon, 2 Sep 2013, Jesper Andersson wrote:
Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser.
J
On 2 Sep 2013, at 15:58, Saad Jbabdi saad@FMRIB.OX.AC.UK wrote:
Hi In Probtrackx, this is done internally.If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better.
Cheers, Saad
On 2 Sep 2013, at 15:56, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani _______________________________________________ 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.-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Thank you! Still somehow I haven't manage to make it work when I ran the suggested command I get an error saying : ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error occurred while parsing element line number: 1 column number: 1. Any advise?
Thanks again
Shani
On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote:
Hi Bruce,
Connectome Workbench commandline utilities can do this with FSL warp fields:
wb_command -surface-apply-warpfield
One needs to use the inverse warp as the <warpfield> argument and the forward warp as the -fnirt <forward-warp>.
Peace,
Matt.
On 9/2/13 11:19 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
A veritable game of telephone! Thanks Jesper. Matt?
On Mon, 2 Sep 2013, Jesper Andersson wrote:
Hi guys, I didn't think we had any tools for doing that, and said so much on the FSL mailbase. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser.
J
On 2 Sep 2013, at 15:58, Saad Jbabdi saad@FMRIB.OX.AC.UK wrote:
Hi In Probtrackx, this is done internally.If you just want to transform the vertex coordinates, then I think you'll need to play with the FNIRT source code - I've CC'd Jesper who knows better.
Cheers, Saad
On 2 Sep 2013, at 15:56, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you might check on the FSL list. I think I've seen some traffic indicating that there are some tools for doing this. I'l cc Saad as he might know cheers Bruce On Mon, 2 Sep 2013, Douglas Greve wrote: Hi Shani, I don't think you can apply a FNIRT transform to a surface. doug On 9/2/13 8:20 AM, Shani Ben Amitay wrote: Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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.-- Saad Jbabdi University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Shani Ben Amitay