Hi, I need to convert a big number of scalar surface maps from fsaverage 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 command line options, but I could not find anything. Is it possible to save and reuse surface transformations?
Best, Chris
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 from fsaverage 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 command line 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 from fsaverage 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 command line 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 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/
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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.
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 from fsaverage > 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 command line > 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
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
16min is a very long time. How many frames are in rh.sig.mgh? For a single frame it should only take 10 or 20 sec
On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
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 mailto: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> <mailto: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 from fsaverage > > 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 command line > > 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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is only one frame in rh.sig.mgh file (see below). Most time seems to be spent in calculating forward and reverse loops. Ideas?
root@36ddc1c5be86:/code# mri_info /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh Volume information for /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000
On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
16min is a very long time. How many frames are in rh.sig.mgh? For a single frame it should only take 10 or 20 sec
On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
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 mailto: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 donot
> have all of the overlays at the same time so I cannot concatenate them. > > To put more contexts: I am building surface support intoneurovault.
> 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 itis
> spend on coregistration - which is always the same. If only I could > calculate the coregistration once and apply it to every incomingmap
> 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> <mailto: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 from fsaverage > > 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 command line > > 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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
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
I found the problem. To save space I only included the surf/{l,r}h.white and surf/{l,r}h.white.reg files in the ICBM2009c_fs6 subejct folder (to save space in my container). After including everything the corregistration run under 10s.
Do you have some ideas which files are speeding up the process?
Best, Chris
On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski < chris.gorgolewski@gmail.com> wrote:
There is only one frame in rh.sig.mgh file (see below). Most time seems to be spent in calculating forward and reverse loops. Ideas?
root@36ddc1c5be86:/code# mri_info /d/drive/workspace/ brainbrowser/examples/models/rh.sig.mgh Volume information for /d/drive/workspace/brainbrowser/examples/models/ rh.sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000
On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
16min is a very long time. How many frames are in rh.sig.mgh? For a single frame it should only take 10 or 20 sec
On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
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 mailto:greve@nmr.mgh.harvard.edu> wrote:
Years ago I used to have code that would cache this transform, butwe
abandoned it because it would get out of synch whenever someone updated their recon, and, for ordinary apps, it does not take that muchtime.
On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote: > Thanks for a quick reply. I'm actually in a situation where I donot
> have all of the overlays at the same time so I cannot concatenate them. > > To put more contexts: I am building surface support intoneurovault.
> 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 itis
> spend on coregistration - which is always the same. If only Icould
> calculate the coregistration once and apply it to every incomingmap
> 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> <mailto: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 from fsaverage > > 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 command line > > 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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
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
I would have thought that it would have crashed without the right files. Or does it go out of the container to get the files it needs? btw, you can use reprozip to see all the files that a process touches to know exactly what it needs
On 11/10/2016 04:10 PM, Chris Filo Gorgolewski wrote:
I found the problem. To save space I only included the surf/{l,r}h.white and surf/{l,r}h.white.reg files in the ICBM2009c_fs6 subejct folder (to save space in my container). After including everything the corregistration run under 10s.
Do you have some ideas which files are speeding up the process?
Best, Chris
On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski <chris.gorgolewski@gmail.com mailto:chris.gorgolewski@gmail.com> wrote:
There is only one frame in rh.sig.mgh file (see below). Most time seems to be spent in calculating forward and reverse loops. Ideas? root@36ddc1c5be86:/code# mri_info /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh Volume information for /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: 16min is a very long time. How many frames are in rh.sig.mgh? For a single frame it should only take 10 or 20 sec On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote: > 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 from > fsaverage > > > 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 > command line > > > 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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > 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>
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Chris Filo Gorgolewski -
Douglas N Greve