Thanks for a prompt reply. The command takes ~16 minutes per hemisphere in my setting. Are those realistic numbers or is it longer than it should take?
mri_surf2surf --s fsaverage --hemi rh --sval /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
sysname Linux hostname 36ddc1c5be86 machine x86_64 user root srcsubject = fsaverage srcval = /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh srctype = trgsubject = ICBM2009c_fs6 trgval = /tmp/out.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading target surface reg /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (157000)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (163842) Reverse Loop had 117731 hits Surf2Surf: Dividing by number of hits (157000) INFO: nSrcLost = 0 nTrg121 = 152424, nTrgMulti = 4576, MnTrgMultiHits = 26.7279 nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985, MnSrcMultiHits = 4.69815 Saving target data Saving to /tmp/out.mgh
real 16m25.129s user 16m24.160s sys 0m0.260s
On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Years ago I used to have code that would cache this transform, but we abandoned it because it would get out of synch whenever someone updated their recon, and, for ordinary apps, it does not take that much time.
On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
Thanks for a quick reply. I'm actually in a situation where I do not have all of the overlays at the same time so I cannot concatenate them.
To put more contexts: I am building surface support into neurovault. When someone uploads a surface statistical map I want to automatically calculate a projection of this map into MNI volume. To improve the MNI volume surface mapping I have reconstructed the surface of the 2009c_asym_nlin template. For every incoming map I am doing fsaverage -> MNI2009c mri_surf2surf followed by mri_surf2vol. However, the mri_surf2surf takes quite a bit of time to run and most of it is spend on coregistration - which is always the same. If only I could calculate the coregistration once and apply it to every incoming map it would speed things up tremendously.
Let me know if you have any ideas.
Best, Chris
On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can use mri_concat to create a stack of overlays, then mri_surf2surf the entire stack, then split the stack. On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote: > Hi, > I need to convert a big number of scalar surface maps fromfsaverage
> to one particular subject space. This means running mri_surf2surf > command many times. For each execution the same transformation is > calculated and then applied. Since estimating the transformation take > a substantial amount of time I was wondering if I could calculate the > transformation once and just apply it (which is a common thing in > volumetric registration). I perused the website and the commandline
> options, but I could not find anything. Is it possible to save and > reuse surface transformations? > > Best, > Chris > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer