Hi Bruce, My problem has been solved. I rotate the ?h.sphere by mris_rotate <source> 0 0 90 <output> and then I used mris_register to register it to fsaverage and I saw my result is perfectly registered to fsaverage. it means that mris_register was not able to realign the sphere to fsaverage if the original orientation is bigger than some degrees like 90. I don't think you need to spend time on it. thanks alot for your helps.
bests Rouhi On Sat, Aug 13, 2011 at 11:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > you can either ftp it or put it on our file drop (you can find both on our > wiki) > > On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: > > where can I upload one subject? which I have problem with that subject in >> RH registraton. >> >> On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> if the aseg is good I don't see how it's possible that we don't know >> about the 90 deg rotation. If you upload the dataset I'll take a look >> On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: >> >> Hi BruceI think the aseg is good but only rotated 90 degree. I >> will try to rotate sphere to see how it will create sphere.reg. >> >> >> >> On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Matt >> >> if they were tipped forward 90deg and we didn't detect it I would >> think that the aseg would fail catastrophically. Did that happen? >> Bruce >> >> On Fri, 12 Aug 2011, Matt Glasser wrote: >> >> >> So I thought the issue had been solved, but perhaps not. Bruce, we >> (i.e. David) think the problem with Rouhi?s data is that FreeSurfer >> did not >> detect that the original images were tipped forward 90 degrees and as >> a result the surface registration failed intermittently (i.e. in >> some >> subjects it okay, but in others it is not). These data were created >> with a fairly old version of FreeSurfer (Rouhi can give the version >> number), >> and then a significant amount of manual effort was put into defining >> some retinotopy on the data. Therefore it isn?t really a feasible >> option to >> just rerun the data with a newer version of FreeSurfer, but we want >> to make use of accurate FreeSurfer surface registration to make group >> average >> retinotopy results. So the question is how do we go about making >> sure the spheres are initialized to have the correct rigid orientation >> before >> the registration proceeds. >> >> >> >> Thanks, >> >> >> Matt. >> >> >> >> >> >> _____________________________**______________________________** >> ______________________________**______________________________** >> __________________________ >> >> >> From: >> freesurfer-boun...@nmr.mgh.**harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu>[mailto: >> freesurfer-bounces@**nmr.mgh.harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu>] >> On Behalf Of Rouhollah Abdollahi >> Sent: Friday, August 12, 2011 12:38 PM >> To: Bruce Fischl >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Label2label on fsaverage >> >> >> >> I tried to rotate the surface by tksurfer and save it as new file . >> But when I open the new surface like white it was not rotated. >> Is there any special thing that I have to do? >> >> Best >> Rouhi >> >> On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi < >> roohy...@gmail.com> wrote: >> >> Dear Bruce >> If I want to rotate sucli pattern too if it is the same? >> >> >> >> >> On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> >> I guess you could rotate the surfaces, save them, then resample the >> labels so that they get the new surface coords and sample them into >> the >> volume, then onto the newly created surfaces. Not sure, we haven't >> ever had to do anything like this. >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think the easiest way is to create all surfaces again but with >> corrected >> and well aligned brain. The next step for me to create new labels >> from old >> labels based on white surface (90 degree rotated) to new white >> surface. But >> how? Is there any way to do that? I mean like label2label or >> surf2surf if >> two surfaces are the same but one of them only rotated?! >> >> Bests >> Rouhi >> >> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> I don't see how anything would work if it was off by 90deg, but >> I guess you should try it >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Because I am using a result from a very old experiment >> that done on wrong direction and the orig.mgz s are not >> oriented according to >> freesurfer template. I cannot creat white because all >> results that I have (label files) are on white surface. >> The only way that I think I need to >> realign all surfaces and volume and apply that rotation on >> my label files. >> >> >> On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> not easily. Why would you need to do such a thing? >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> >> I have a data set which I can not create the white >> surfaces because all of my results are according to white >> surface. I would >> like to know is >> there any way to rotate all surfaces and volumes and >> labels ... (everything) after finishing recon-all process. >> like 90 degree >> around X axis? >> and apply this rotation to all data set? >> >> Best >> Rouhi >> >> >> On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Rouhi >> >> I don't really understand. Are you saying you >> transformed the initial image before giving it to >> recon-all? There is a >> switch to >> mris_register to initialize with the tal xform, >> but we never use it as in pretty extensive tests it didn't >> seem to help. >> mris_register has a very large initial capture >> range due to it's global search, so I would be surprised >> if the initial >> orientation >> was the problem. >> >> cheers >> Bruce >> >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think I found the problem. The problem came >> from the original oriantation of T1 image and I think >> mris_register could >> not >> find it itself during >> the recon-all. I added to have initial alignment >> to inflated and the problem solved.( mris_register -curve >> -inflated >> ?h.sphere <template >> target> ?h.sphere.reg ) I think it is very >> important to add it to recon-all because if the user >> doesn't know the real >> oriantation it might make >> such a problem. >> >> Thanks for your quick response. >> >> On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah >> Abdollahi <roohy...@gmail.com> wrote: >> Dear Bruce >> >> I am working on Freesurfer 2 caret meshes. >> I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh >> from Van Essen lab >> to >> create caret >> surfaces. when I look at my subjects' >> surfaces I can see in flat map in caret some of subjects >> sulci patterns are >> really >> distorted >> and I think it is related to >> sphere registration to fsaverage sphere. Beacsue the code >> is using sphere.reg to create >> all >> surfaces. >> for the subjects which I have less >> distortion on sulci pattern I have good data (3 subjects) >> but for the (9 >> subjects) >> rest it seems >> they have problem to register to fsaverage. >> Is there any way that I can be sure that >> sphere.reg properly created? >> >> Thank you very much >> >> Rouhi >> >> >> >> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah >> Abdollahi <roohy...@gmail.com> wrote: >> >> > .V1_reg.label --regmethod surface >> --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and >> when I tried to load >> the >> output >> label file on fsaverage surface like >> inflated one it shows a lot of point looks like it is not >> deformed properly. Is >> it >> related >> to registration to fsaverage or something >> esle? The question is how I can register the subjects >> surfaces to fsaverage >> surfaces? >> -- With Best Regards Rouhi >> --**0015175120c69a3c6804aa2ffb81 Content-Type: text/html; >> charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> Dear freesurfer experts >> > >> > I've tried to export my label file from >> individual space to fsaverage space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label >> --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or >> something esle? >> > The question is how I can register the >> subjects surfaces to fsaverage >> >> >> 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. >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> -- >> >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> -- With Best Regards Rouhollah Abdollahi
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