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
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