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 fischl@nmr.mgh.harvard.eduwrote:
What format is the attachment in?
On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi roohy466@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 <fischl@nmr.mgh.harvard.edu fischl@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 <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce
On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <<roohy466@gmail.com>roohy466@gmail.com> wrote:
> .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfregsphere.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/compliancelinehttp://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>
Hi Rouhi
you can specify -norot to disable the initial rotation, but I wouldn't think that would be a good thing to do. To decrease distortion you would increase the strength of the metric term using -dist <float>. The default is 5, so you could try raising it to 10 or 15.
cheers Bruce
On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote:
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 fischl@nmr.mgh.harvard.edu wrote: What format is the attachment in?
On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi roohy466@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 <fischl@nmr.mgh.harvard.edu> wrote: Hi Rouhi check the parcellations. If they are correct then the sphere.reg must be pretty accurate. cheers BruceOn Thu, 11 Aug 2011, Rouhollah Abdollahi wrote:
Dear Bruce I am working on Freesurfer 2 caret meshes. I am using FreeSurfer2CaretConvertAndRegisterClean.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 <fischl@nmr.mgh.harvard.edu> wrote: Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466@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 . 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Rouhollah Abdollahi