Hi Doug So all of my overlays for each subject have been registered to fsaverage using mri_surf2surf. I am now wondering how I could create an average in "fsaverage space" using these overlays - I understand that mris_make_average_surface is an option but I cannot seem to find whether this works for overlays and not just surfaces (white, pial). I want to take each subject overlay on fsaverage and average them to get a probability map.
thanks -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > So all of my sulci for each subject have been registered to fsaverage > using mri_surf2surf. I am now wondering how I could create an average of a > sulcus using these overlays - I understand that mris_make_average_surface > is an option but I cannot seem to find whether this works for overlays and > not just surfaces (white, pial). I want to take each subject overlay on > fsaverage and average them to get a probability map for a single sulcus. > > thanks > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much < > trisanna.sprung-m...@mail.mcgill.ca> wrote: > >> worked beautifully. Thank you! >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> Try surf2surf with --mapmethod nnf >>> >>> On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote: >>> > Hi Doug - yes they do actually, I was quite pleased. I did some trials >>> > with other subjects and the mri_vol2surf all looks good. Very similar >>> > to what I had in our in-house software. >>> > >>> > Would things be better if I were to isolate each sulcus as a .label >>> > and then try the mri_label2label? Someone suggested perhaps the >>> > colours are overlapping with the overlay.... >>> > >>> > -- >>> > Ph.D. Candidate >>> > McGill University >>> > Integrated Program in Neuroscience >>> > Psychology >>> > >>> > >>> > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve >>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> > >>> > The problem is probably that the vol2surf command did not properly >>> > sample the labels onto the surface. Do the labels on subject 00350 >>> > surfaces look ok? >>> > >>> > On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote: >>> > > thanks Dr. Fischl >>> > > >>> > > So the command seems to have worked! I have copied what ran in my >>> > > terminal. When I open the test.mgz overlay on the fsaverage pial >>> > > surface, things look ok but a bit funny. I am wondering if there >>> is >>> > > anything I can do to the mri_surf2surf command to improve the >>> > > registration to fsaverage? *See my snapshots attached.* >>> > > >>> > > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval >>> > > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >>> > > --trgsubject fsaverage --tval test.mgz --hemi lh >>> > > srcsubject = 00350 >>> > > srcval = >>> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >>> > > srctype = >>> > > trgsubject = fsaverage >>> > > trgval = test.mgz >>> > > 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/00350/surf/lh.sphere.reg >>> > > Loading source data >>> > > 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 (166912) >>> > > Reverse Loop had 41306 hits >>> > > Surf2Surf: Dividing by number of hits (163842) >>> > > INFO: nSrcLost = 0 >>> > > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749 >>> > > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, >>> MnSrcMultiHits = >>> > > 2.28602 >>> > > Saving target data >>> > > Saving to test.mgz >>> > > >>> > > best >>> > > >>> > > Trisanna >>> > > >>> > > -- >>> > > Ph.D. Candidate >>> > > McGill University >>> > > Integrated Program in Neuroscience >>> > > Psychology >>> > > >>> > > >>> > > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl >>> > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> >>> > <mailto:fis...@nmr.mgh.harvard.edu >>> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >>> > > >>> > > Hi Trisanna >>> > > >>> > > you would only use those options of if you were transforming >>> > a surface >>> > > Bruce >>> > > >>> > > >>> > > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: >>> > > >>> > > thanks Dr. Fischl >>> > > >>> > > I assume that for surface overlays one cannot specify >>> > > --sval-xyz and --tval-xyz or the command will treat the >>> > input >>> > > as a surface >>> > > itself? >>> > > >>> > > best >>> > > >>> > > Trisanna >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > > Ph.D. CandidateMcGill University >>> > > Integrated Program in Neuroscience >>> > > Psychology >>> > > >>> > > >>> > > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl >>> > > <fis...@nmr.mgh.harvard.edu >>> > <mailto:fis...@nmr.mgh.harvard.edu> >>> > > <mailto:fis...@nmr.mgh.harvard.edu >>> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >>> > > Hi Trisanna >>> > > >>> > > you don't need to inflate the overlays. They can >>> just >>> > > use the existing surface-based (sphere.reg) registration. >>> > > >>> > > cheers >>> > > Bruce >>> > > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote: >>> > > >>> > > Hi there >>> > > So I have sulcal labels from another software >>> > > (.mnc format) from which I am trying to generate some >>> > > probability maps. I was able >>> > > to convert the .mnc to .mgz surface overlay >>> > using >>> > > mri_vol2surf for my MRIs after running all MRIs in >>> > > recon-all. So, now I have >>> > > all my painted voxels as surface overlays, >>> as I >>> > > was instructed to do a few months ago. >>> > > >>> > > I was told that the next step would be to use >>> > > mri_surf2surf to resample the overlays to fsaverage. >>> > > >>> > > I am a bit confused as I would think that >>> > the next >>> > > step would be to take the surface overlays and >>> > > inflate them before I register >>> > > them to fsaverage. I see that when recon-all >>> > runs, >>> > > it computes the registration of the MRI surface to >>> > > fsaverage and saves it as >>> > > sphere.reg. Is there a way I can inflate my >>> > > surface overlays in a similar manner and then apply this >>> > > same registration to my >>> > > surface overlays? Or am I missing something? >>> > > >>> > > thanks very much! >>> > > >>> > > Trisanna >>> > > >>> > > >>> > > -- >>> > > Ph.D. CandidateMcGill 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 >>> > > >>> > > >>> > > 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> >>> > <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 >>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > 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 >>> gr...@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 >>> >> >> >
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