Dear FS experts,
I have some troubles when I'm trying to use the command mris_spherical_average.
Once I have a X.label defined for all my subjects in their native space, I used mri_label2label to put all my label files in fsaverage (--trgsubject fsaverage) ? Then I ran : mris_spherical_average label lh.X lh sphere.reg s1sn lh.Xproba.label in order to create a probabilistic map as you did in this paper : "Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI".
When I loaded the output label in fsaverage I obtained this image but I expected a label in heschl gyrus
Do you have any idea to fix this ? Should I use label2label to put all files in a common space or not ? Which spherical surface should I use in the command mris_spherical_average ?
Best regards.
Sophie Maingault
Hi Sophie
mris_spherical_average is an alternative to mri_label2label and takes labels in the individual subject spaces, not fsaverage.
cheers Bruce On Thu, 30 Jan 2014, Sophie Maingault wrote:
Dear FS experts,
I have some troubles when I'm trying to use the command mris_spherical_average.
Once I have a X.label defined for all my subjects in their native space, I used mri_label2label to put all my label files in fsaverage (--trgsubject fsaverage) ? Then I ran : mris_spherical_average label lh.X lh sphere.reg s1…sn lh.Xproba.label in order to create a probabilistic map as you did in this paper : "Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI".
When I loaded the output label in fsaverage I obtained this image but I expected a label in heschl gyrus…
Do you have any idea to fix this ? Should I use label2label to put all files in a common space or not ? Which spherical surface should I use in the command mris_spherical_average ?
Best regards.
Sophie Maingault
[IMAGE]
Ok thanks. So I ran mris_spherical_average label lh lh.X lh sphere.reg s1sn output.label with lh.X.label label files in the individual subject spaces (without doing label2label before). But when I tried to display the label in fsaverage I have something weird, the text file seems good but the vertices are not localized at the right places. I think I did a mistake either for the spherical surface in the command or either for the image used for display.
Best regards. Sophie
Le 30/01/14 14:42, « Bruce Fischl » fischl@nmr.mgh.harvard.edu a écrit :
Hi Sophie
mris_spherical_average is an alternative to mri_label2label and takes labels in the individual subject spaces, not fsaverage.
cheers Bruce On Thu, 30 Jan 2014, Sophie Maingault wrote:
Dear FS experts,
I have some troubles when I'm trying to use the command mris_spherical_average.
Once I have a X.label defined for all my subjects in their native space, I used mri_label2label to put all my label files in fsaverage (--trgsubject fsaverage) ? Then I ran : mris_spherical_average label lh.X lh sphere.reg s1sn lh.Xproba.label in order to create a probabilistic map as you did in this paper : "Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI".
When I loaded the output label in fsaverage I obtained this image but I expected a label in heschl gyrus
Do you have any idea to fix this ? Should I use label2label to put all files in a common space or not ? Which spherical surface should I use in the command mris_spherical_average ?
Best regards.
Sophie Maingault
[IMAGE]
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.
Hi Sophie
can you visualize each of the individual subject labels to make sure that they look ok? You also need to specify -o fsaverage to use fsaverage as the output subject, otherwise it will assume that the last subject in your list is the output subject (this is why your output label doesn't look correct on the fsaverage surface)
cheers Bruce
On Thu, 30 Jan 2014, Sophie Maingault wrote:
Ok thanks. So I ran mris_spherical_average label lh lh.X lh sphere.reg s1?sn output.label with lh.X.label label files in the individual subject spaces (without doing label2label before). But when I tried to display the label in fsaverage I have something weird, the text file seems good but the vertices are not localized at the right places. I think I did a mistake either for the spherical surface in the command or either for the image used for display.
Best regards. Sophie
Le 30/01/14 14:42, « Bruce Fischl » fischl@nmr.mgh.harvard.edu a écrit :
Hi Sophie
mris_spherical_average is an alternative to mri_label2label and takes labels in the individual subject spaces, not fsaverage.
cheers Bruce On Thu, 30 Jan 2014, Sophie Maingault wrote:
Dear FS experts,
I have some troubles when I'm trying to use the command mris_spherical_average.
Once I have a X.label defined for all my subjects in their native space, I used mri_label2label to put all my label files in fsaverage (--trgsubject fsaverage) ? Then I ran : mris_spherical_average label lh.X lh sphere.reg s1?sn lh.Xproba.label in order to create a probabilistic map as you did in this paper : "Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI".
When I loaded the output label in fsaverage I obtained this image but I expected a label in heschl gyrus?
Do you have any idea to fix this ? Should I use label2label to put all files in a common space or not ? Which spherical surface should I use in the command mris_spherical_average ?
Best regards.
Sophie Maingault
[IMAGE]
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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