Hi there
I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data.
Below is the command that I ran. Is there something I am missing here?
many thanks
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
I don't understand what you did or what the problem is. Can you elaborate?
On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:
Hi there
I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data.
Below is the command that I ran. Is there something I am missing here?
many thanks
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
What I mean to say is that the pial surface created by recon-all and the pial surface that has been nonlinearly registered to fsaverage look pretty much identical in sulcal patterns, but I do not understand how this can be the case if one surface has been registered to a surface template based on cortical folding. Shouldn't the cortical folding for this registered surface change even a little bit?
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jul 19, 2016 at 10:29 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I don't understand what you did or what the problem is. Can you elaborate?
On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:
Hi there
I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data.
Below is the command that I ran. Is there something I am missing here?
many thanks
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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So if I understand, you used mri_surf2surf to map the curv from your subject to fsaverage. You then viewed the original curv on the original subject and then you viewed the fsaveage-mapped curv on faverage and you find that they are very similar. Is that right? This would not surprise me much. If you still have questions, pictures would help alot
On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote:
Hi Doug
What I mean to say is that the pial surface created by recon-all and the pial surface that has been nonlinearly registered to fsaverage look pretty much identical in sulcal patterns, but I do not understand how this can be the case if one surface has been registered to a surface template based on cortical folding. Shouldn't the cortical folding for this registered surface change even a little bit?
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jul 19, 2016 at 10:29 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't understand what you did or what the problem is. Can you elaborate? On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below is the command that I ran. Is there something I am missing here? many thanks Trisanna trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 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.
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Hi Doug
not quite - I used mri_surf2surf *with the pial surfaces* and then when I compared the original pial with the registered pial they look pretty much the same. I followed an example from mri_surf2surf --help.
See the command output and attached jpgs.
If a surface is registered to a surface template, in my mind this would mean that the cortical folding (i.e. the actual sulci) would differ afterwards but I guess this is not the correct line of thinking?
best
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
So if I understand, you used mri_surf2surf to map the curv from your subject to fsaverage. You then viewed the original curv on the original subject and then you viewed the fsaveage-mapped curv on faverage and you find that they are very similar. Is that right? This would not surprise me much. If you still have questions, pictures would help alot
On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote:
Hi Doug
What I mean to say is that the pial surface created by recon-all and the pial surface that has been nonlinearly registered to fsaverage look pretty much identical in sulcal patterns, but I do not understand how this can be the case if one surface has been registered to a surface template based on cortical folding. Shouldn't the cortical folding for this registered surface change even a little bit?
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jul 19, 2016 at 10:29 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't understand what you did or what the problem is. Can you elaborate? On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below is the command that I ran. Is there something I am missing here? many thanks Trisanna trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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The only thing you are doing with this command is to change the number and identity of the vertices, the xyz will not change at all and so the appearance of the surface will not change (much).
On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote:
Hi Doug
not quite - I used mri_surf2surf *with the pial surfaces* and then when I compared the original pial with the registered pial they look pretty much the same. I followed an example from mri_surf2surf --help.
See the command output and attached jpgs.
If a surface is registered to a surface template, in my mind this would mean that the cortical folding (i.e. the actual sulci) would differ afterwards but I guess this is not the correct line of thinking?
best
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So if I understand, you used mri_surf2surf to map the curv from your subject to fsaverage. You then viewed the original curv on the original subject and then you viewed the fsaveage-mapped curv on faverage and you find that they are very similar. Is that right? This would not surprise me much. If you still have questions, pictures would help alot On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote: > Hi Doug > > What I mean to say is that the pial surface created by recon-all and > the pial surface that has been nonlinearly registered to fsaverage > look pretty much identical in sulcal patterns, but I do not understand > how this can be the case if one surface has been registered to a > surface template based on cortical folding. > Shouldn't the cortical folding for this registered surface change even > a little bit? > > best > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Jul 19, 2016 at 10:29 PM, Douglas 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: > > I don't understand what you did or what the problem is. Can you > elaborate? > > > On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote: >> Hi there >> >> I tested registering a subject's pial surface to fsaverage and >> compared the original pial (from recon-all) with this registered >> pial surface. It turns out that they are almost identical in >> nature, and I am wondering how this is possible if recon-all does >> not alter the input data. >> >> Below is the command that I ran. Is there something I am missing >> here? >> >> many thanks >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz >> pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 >> --hemi lh >> srcsubject = icbm-102 >> srcval = (null) >> srctype = >> trgsubject = fsaverage >> trgval = lh.pial.icbm102 >> trgtype = >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg >> Loading source data >> Reading surface file >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Reading target surface reg >> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg >> Done >> Mapping Source Volume onto Source Subject Surface >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (163842) >> >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (169941) >> Reverse Loop had 44416 hits >> Surf2Surf: Dividing by number of hits (163842) >> INFO: nSrcLost = 0 >> nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 >> nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, >> MnSrcMultiHits = 2.28035 >> Saving target data >> >> >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 > > > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug
Is this what is meant by the example with --help? "Convert the surface coordinates" to me sounds as if it would change the x,y,z of the vertices... Additionally, when I watching the online tutorials surface registration was explained as "aligning the anatomy" so I totally missed that it doesn't change the x,y,z of the vertices.
3. Convert the surface coordinates of the lh.white of a subject to a (talairach) average (ie, a subject created by make_average_subject):
mri_surf2surf --s yoursubject --hemi lh --sval-tal-xyz white --tval lh.white.yoursubject --tval-xyz --trgsubject youraveragesubject
This will create youraveragesubject/surf/lh.white.yoursubject
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Jul 21, 2016 at 1:16 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The only thing you are doing with this command is to change the number and identity of the vertices, the xyz will not change at all and so the appearance of the surface will not change (much).
On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote:
Hi Doug
not quite - I used mri_surf2surf *with the pial surfaces* and then when I compared the original pial with the registered pial they look pretty much the same. I followed an example from mri_surf2surf --help.
See the command output and attached jpgs.
If a surface is registered to a surface template, in my mind this would mean that the cortical folding (i.e. the actual sulci) would differ afterwards but I guess this is not the correct line of thinking?
best
Trisanna
trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So if I understand, you used mri_surf2surf to map the curv from your subject to fsaverage. You then viewed the original curv on the original subject and then you viewed the fsaveage-mapped curv on faverage and you find that they are very similar. Is that right? This would not surprise me much. If you still have questions, pictures would help alot On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote: > Hi Doug > > What I mean to say is that the pial surface created by recon-alland
> the pial surface that has been nonlinearly registered to fsaverage > look pretty much identical in sulcal patterns, but I do not understand > how this can be the case if one surface has been registered to a > surface template based on cortical folding. > Shouldn't the cortical folding for this registered surface change even > a little bit? > > best > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Jul 19, 2016 at 10:29 PM, Douglas 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: > > I don't understand what you did or what the problem is. Can you > elaborate? > > > On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote: >> Hi there >> >> I tested registering a subject's pial surface to fsaverage and >> compared the original pial (from recon-all) with this registered >> pial surface. It turns out that they are almost identical in >> nature, and I am wondering how this is possible if recon-all does >> not alter the input data. >> >> Below is the command that I ran. Is there something I am missing >> here? >> >> many thanks >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz >> pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 >> --hemi lh >> srcsubject = icbm-102 >> srcval = (null) >> srctype = >> trgsubject = fsaverage >> trgval = lh.pial.icbm102 >> trgtype = >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg >> Loading source data >> Reading surface file >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Reading target surface reg >> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg >> Done >> Mapping Source Volume onto Source Subject Surface >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (163842) >> >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (169941) >> Reverse Loop had 44416 hits >> Surf2Surf: Dividing by number of hits (163842) >> INFO: nSrcLost = 0 >> nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 >> nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, >> MnSrcMultiHits = 2.28035 >> Saving target data >> >> >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 > > > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Douglas Greve -
Douglas N Greve
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Trisanna Sprung-Much