External Email - Use Caution
Hi Jan
If you create a family template you will only be able to compare within family,
unless you also align the templates I guess?
-nonorm will disable z-normalization of curv and sulc. We typically start with
a single subject atlas, do a nonlinear (but highly regularized) warp to it,
then rebuild the atlas and re-register. We do have a prototype of a more
principled procedure but it won't be ready for a few months
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Koten, Jan Willem
(jan.ko...@uni-graz.at)
Sent: Monday, May 8, 2023 8:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_register options
External Email - Use Caution
Dear Doug
Dear Bruce
Martin Reuter suggested me to write you since you are familiar with true inner
workings of free surfer. In my project I try to create a family specific
template that is based on three or more family members. We try to avoid the
bias that may arise by choosing one family member as a target. There is
procedure that tries to this described in:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1IEewrYydOjuYqfmmr7slT8MnQVuTxf5Fupk3DeKFnIOTz1DEFj2XEjEdyBGl0H82UxlCdqEDOvd2EDHAlZHMPFrLfgUiVpijFeEqiemSYey9I4nvk62Ghs7tu2PJB3D_s71OfS1MCH9QDnN1wtgDEOhDxB5QMNr5Z_b6A8aFE3WVMD_08wVNsXG7iSsVyQqNaYynws6DKBeVujNvubb93pSBqcIDoN496yyjtuK-59Y9WSWfgvXyb-MvrrVcK4yB/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FSurfaceRegAndTemplates<https://secure-web.cisco.com/1Blsa_5fBePXLqTD4MyXB0MVZ8BfrqXwEgfuiFRtv-42VQP34OZ6UZqdfXxQi0tp2V1EoRTro-xOcgb7ClgzFVab407J4Z41cRtu_iJQ7EKKFe0dAvW9s60J_gwqS1U2oxlZRIad20a0m-SEzzq_ngB-95XOOsQpMhOfq6ISgUdxzB8ogeIbf9x0lfc2JgBeXKvf1G9CU7-7m6bSre4_KnhmyXHwl-5_eSx-dnrYxMX7JAnXnHbhmjXzfh_iBpIw7lCaHPbppGijCuVEpwx63sC4TUffSW5dEK1Gxyynbnu8l0ZQdcwiR0kzFZjQvXTtAQikt0tdUkeVQhN8lPE8JlA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FSurfaceRegAndTemplates>
We found out that family specific templates result in better alignment among
family members when compared to the standard fs average template. The creation
of a template depends on the mris_register command that has several options
that can be manipulated. However, we do not know what those options are doing
in detail
What is the initial sulcal alignment? Is this a rigid alignment procedure?
Maybe a hard spherical rotation based on least squares algorithms?
What is the final curve alignment? Is this a non-linear alignment procedure?
If sulcal alignment is rigid, why does it take three times as long as
non-linear curv alignment?
What is normalization in context of mris_register which can be disabled trough
the -nonorm step?
Does the spring factor affect how much the Individual scul/curv maps are
aligned with the family template? And if the latter is the case what is a
reasonable spring value if you want to obtain individuals that are as closely
matched to the family template as possible?
Thank you in Advance
Many greetings from Austria
Jan
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
