Hi Doug, Still no luck getting the script- the site does not load for some reason. Any chance you might be able to paste it into the message body?
Thanks, - Arkadiy On Sun, Jun 19, 2016 at 12:00 PM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: GLM_Fit Question (Douglas Greve) > 2. Using Freesurfer commands in matlab (HARI GURAGAIN) > 3. change the algorithm (N Saf) > 4. Re: change the algorithm (Bruce Fischl) > 5. Re: registering to fsaverage (Trisanna Sprung-Much) > 6. Re: registering to fsaverage (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jun 2016 23:54:18 +0200 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] GLM_Fit Question > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <5765c30a.5080...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > try now > > On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: > > Hi Freesurfers, > > > > I am having a similar problem with the FSGD file as the user indicated > > at this thread: > > > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html > > > > I am trying to access the script that Doug wrote in order to fix it, > > however, the link to download the script does not seem to be working. > > I was wondering if someone might be able to upload it again. > > > > Thank you in advance for your help, > > > > Arkadiy > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160618/91a648b5/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sat, 18 Jun 2016 18:02:26 -0500 > From: HARI GURAGAIN <nuclear.h...@gmail.com> > Subject: [Freesurfer] Using Freesurfer commands in matlab > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > cadp7hjx6qhmjov1gzmckdmg7vhma439wkqg81unyjgkzfjz...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Freesurfer, > > I am using the new development version of freesurfer ( > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev). > I am trying to call some of the freesurfer commands like: mri_coreg or some > other. When I use the something like the following in Matlab: > command='/Applications/freesurfer/bin/mri_coreg' > and the below: > [status,cmdout]=system(command) > It is showing a weird error message like below: > ########################################### > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > ########################################### > I really don't understand why this error is coming. I have seen people have > used the mri_*** commands a lot of times in matlab but unfortunately, it > shows the above error in my case. > Is it the error from Matlab, freesurfer, mac or something else? > > Any help in solving this issue will be greatly appreciated. > > Thank you. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160618/dfe5fbce/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Sun, 19 Jun 2016 12:06:56 +0430 > From: N Saf <nali...@gmail.com> > Subject: [Freesurfer] change the algorithm > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > < > capmqmelhyw65v+yhsbxseksx-esbvw1t6mqa5dp9sps5n4l...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Freesurfer, > > I wonder if it is possible to segment just one sub-cortical structures like > hippocampus by changing the algorithm (e.g. according to spatial prior > knowledge divided the image to some sub-images and do analysis just on that > sub-image which we sure the hippocampus located)and by that reducing the > processing time ? and another general question I have is that in > sub-cortical segmentation commands 1to12 commands of -all flag which > parameters can I change to affect the outputs? > > Sincerely, > Nazanin > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160619/bedba579/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Sun, 19 Jun 2016 10:51:58 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] change the algorithm > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1606191050540.7...@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Nazanin > > no, sorry, that isn't possible. Our accuracy is improved by the fact that > we model all subcortical structures simultaneously. > > As for your second question you need to be more specific. Are you finding > some inaccuracies that you want to correct? > > cheers > Bruce > > > On Sun, 19 Jun 2016, N Saf wrote: > > > Dear Freesurfer, > > > > I wonder if it is possible to segment just one sub-cortical structures > like > > hippocampus by changing the algorithm (e.g. according to spatial prior > > knowledge divided the image to some sub-images and do analysis just on > that > > sub-image which we sure the hippocampus located)and by that reducing the > > processing time ? and another general question I have is that in > > sub-cortical segmentation commands 1to12 commands of -all flag? which > > parameters can I change to affect the outputs? > > > > Sincerely, > > Nazanin > > > > ? > > > > > > ------------------------------ > > Message: 5 > Date: Sun, 19 Jun 2016 11:17:54 -0400 > From: Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca> > Subject: Re: [Freesurfer] registering to fsaverage > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > cag+torurx1_5wjpo0qh4ebabi1wwqr-na0d8i76awb_fquw...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > >>> > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160619/eeefc635/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Sun, 19 Jun 2016 11:22:41 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] registering to fsaverage > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1606191121510.7...@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Trisanna > > Doug is on vacation and his response time is likely to be pretty slow. If > any emails go unanswered you should repost them in a week or two. > > As for this, if you overlays are mapped to fsaverage you can just use > mri_average to average them. > > cheers > Bruce > > > > On Sun, 19 > Jun 2016, Trisanna Sprung-Much wrote: > > > 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. CandidateMcGill 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. CandidateMcGill 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. CandidateMcGill 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 > > > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 148, Issue 28 > ******************************************* >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
