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
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