Dear Bruce, I have two questions. I saw there are a lot of algorithms for mris_register. Which one are more precise and has less distortion on sulci pattern? In initial alignment if I want to rotate the surface with -rotate [ alpha is (ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that mris_register does not apply any rigid alignment after initial rotation what I have to do?
Thanks Rouhi On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > What format is the attachment in? > > > > On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi <roohy...@gmail.com> > wrote: > > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , > whcih subj_1 shows bad registration to fsaverage and subj_2 shows the good > registration. I attached a file which compare two subjects according to > sphere and sphere.reg. For the subj_1 , it has more figures to see how the > parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <<fis...@nmr.mgh.harvard.edu> > fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Rouhi >> >> check the parcellations. If they are correct then the sphere.reg must be >> pretty accurate. >> >> cheers >> Bruce >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi 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> >>> 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> >>> 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 > > > > <subject_1&2_side_view.odp> > > -- With Best Regards Rouhollah Abdollahi
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