Hello all,
We are having trouble with the output after running recon-all -all -subjid subjectx on our scans.
Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe.
After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 -cp -autorecon3 -subjid subjects.
This made the the left lobe look better, but then we spotted new missing bits on the right side
anterior temporal lobe.
Any ideas on dealing with these missing temporal lobe issues?
Thanks,
Eileen Daly
Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce
On May 20, 2014, at 9:34 AM, "Daly, Eileen" eileen.daly@kcl.ac.uk wrote:
Hello all,
We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe.
After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 –cp -autorecon3 -subjid subjects.
This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe.
Any ideas on dealing with these missing temporal lobe issues?
Thanks,
Eileen Daly _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi there, I tried to put more CP, so all the temporal lobe tissue is in the mask. This will end up in overestimation of white matter. So in a second step you will have to manually adjust WM mask. In my dataset, after adjusting WM mask, WM ist still little bit oversetimated, but at least i am not missing tissue. When you find a better option, I am glad to learn about. Good luck!
Best, Kristina ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 22. Mai 2014 04:35 An: Freesurfer support list Betreff: Re: [Freesurfer] missing temporal lobes
Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce
On May 20, 2014, at 9:34 AM, "Daly, Eileen" eileen.daly@kcl.ac.uk wrote:
Hello all,
We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe.
After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 –cp -autorecon3 -subjid subjects.
This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe.
Any ideas on dealing with these missing temporal lobe issues?
Thanks,
Eileen Daly _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.
Hi Kristina
that shouldn't be needed. If you upload a dataset we will take a look
cheers Bruce On Thu, 22 May 2014, Mayer Kristina wrote:
Hi there, I tried to put more CP, so all the temporal lobe tissue is in the mask. This will end up in overestimation of white matter. So in a second step you will have to manually adjust WM mask. In my dataset, after adjusting WM mask, WM ist still little bit oversetimated, but at least i am not missing tissue. When you find a better option, I am glad to learn about. Good luck!
Best, Kristina ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 22. Mai 2014 04:35 An: Freesurfer support list Betreff: Re: [Freesurfer] missing temporal lobes
Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce
On May 20, 2014, at 9:34 AM, "Daly, Eileen" eileen.daly@kcl.ac.uk wrote:
Hello all,
We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe.
After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 –cp -autorecon3 -subjid subjects.
This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe.
Any ideas on dealing with these missing temporal lobe issues?
Thanks,
Eileen Daly _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Daly, Eileen -
Mayer Kristina