Dear Freesurfer users, I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc).What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know. By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool! Cheers,Marco
Hi Marco
I believe that we made that figure by importing the registered spheres into photoshop and using the magic wand to outline the sulc boundaries. If your goal is just seeing if the registration worked there are easier ways to do it
cheers Bruce
On Sun, 5 Mar 2017, Marco Martinolli wrote:
Dear Freesurfer users,
I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc). What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know.
By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool!
Cheers, Marco
Thank you Bruce.
So could you give me some of these alternative ideas to see the quality of the registration?
Cheers, Marco
Inviato da iPhone
Il giorno 05 mar 2017, alle ore 19:27, Bruce Fischl fischl@nmr.mgh.harvard.edu ha scritto:
Hi Marco
I believe that we made that figure by importing the registered spheres into photoshop and using the magic wand to outline the sulc boundaries. If your goal is just seeing if the registration worked there are easier ways to do it
cheers Bruce
On Sun, 5 Mar 2017, Marco Martinolli wrote:
Dear Freesurfer users, I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc). What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know. By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool! Cheers, Marco
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look at the aparc is a good place to start. You can also save tiff snapshots in freeview of each subject with the sulc or curv overlaid on the sphere.reg, then zip through them all with nmovie.
cheers Bruce On Sun, 5 Mar 2017, Marco Martinolli wrote:
Thank you Bruce.
So could you give me some of these alternative ideas to see the quality of the registration?
Cheers, Marco
Inviato da iPhone
Il giorno 05 mar 2017, alle ore 19:27, Bruce Fischl fischl@nmr.mgh.harvard.edu ha scritto:
Hi Marco
I believe that we made that figure by importing the registered spheres into photoshop and using the magic wand to outline the sulc boundaries. If your goal is just seeing if the registration worked there are easier ways to do it
cheers Bruce
On Sun, 5 Mar 2017, Marco Martinolli wrote:
Dear Freesurfer users, I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc). What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know. By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool! Cheers, Marco
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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Bruce Fischl -
Marco Martinolli