Re: [Freesurfer] generating new FREESURFER directory from linear transform
yes, it is doable in principle. We have tools for transforming volumes and surfaces - you just have to apply them to everything Bruce On Thu, 10 Sep 2015, David Grayson wrote: Hey Bruce, Thanks for your response - is it in principle possible to achieve what I want by applying the transform to the segmentations and surface files and then running the latter stages of recon-all to regenerate the parcellations and stats? Or is there a reason you might foresee that this simply won't work in a piecemeal fashion either? Wondering if it's even worth going down this rabbit hole... Thanks again, David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, September 04, 2015 5:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] generating new FREESURFER directory from linear transform Hi David I don't think there's an easy way to do it all at once unless you apply the transform to the orig.mgz then rerun recon-all (which will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: Hi all, I would like to take a single subject’s freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new freesurfer directory that keeps as much of the same contents as possible. The transform is not just rigid-body, it includes scaling and skewing. Is there a suggested way to do this, either all-at-once or piece-by-piece? Thank you very much, David ___ 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.
Re: [Freesurfer] generating new FREESURFER directory from linear transform
Hey Bruce, Thanks for your response - is it in principle possible to achieve what I want by applying the transform to the segmentations and surface files and then running the latter stages of recon-all to regenerate the parcellations and stats? Or is there a reason you might foresee that this simply won't work in a piecemeal fashion either? Wondering if it's even worth going down this rabbit hole... Thanks again, David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, September 04, 2015 5:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] generating new FREESURFER directory from linear transform Hi David I don't think there's an easy way to do it all at once unless you apply the transform to the orig.mgz then rerun recon-all (which will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: > > Hi all, > > > > I would like to take a single subject’s freesurfer directory and apply > a single linear transform (I already have the .dat file I would like > to use) to all of the recon-all output (volumes, surfaces, label files, etc). > Essentially I would like to apply the transform and make a new > freesurfer directory that keeps as much of the same contents as > possible. The transform is not just rigid-body, it includes scaling and > skewing. > > > > Is there a suggested way to do this, either all-at-once or piece-by-piece? > > > > Thank you very much, > > > > David > > > > > ___ 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] generating new FREESURFER directory from linear transform
Hi all, I would like to take a single subject's freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new freesurfer directory that keeps as much of the same contents as possible. The transform is not just rigid-body, it includes scaling and skewing. Is there a suggested way to do this, either all-at-once or piece-by-piece? Thank you very much, David ___ 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.
Re: [Freesurfer] generating new FREESURFER directory from linear transform
Hi David I don't think there's an easy way to do it all at once unless you apply the transform to the orig.mgz then rerun recon-all (which will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: Hi all, I would like to take a single subject’s freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new freesurfer directory that keeps as much of the same contents as possible. The transform is not just rigid-body, it includes scaling and skewing. Is there a suggested way to do this, either all-at-once or piece-by-piece? Thank you very much, David ___ 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.
