You just need to rerun mris_register using the options I included in my
previous email. This will recreate the ?h.sphere.reg, after which you can
recreate the parcellation
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Fraser Smith
Sent: Monday, April 26, 2021 9:33 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L
Hemisphere
External Email - Use Caution
Thanks Bruce - getting back to this after quite some time now. I've managed to
make a central sulcus label file following these instructions (turns out the CS
was connected to the Post CS) and run it through mris-register.
I had a couple of follow up questions:
How can I use the results of the above to create a corrected parcellation? I
presume I need to recreate surfaces / labels afterwards - which command should
I use for this?
best
Fraser
On Fri, Mar 13, 2020 at 2:34 PM Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Fraser
if you look at the mris_register help there is an option to specify a
manual label that corresponds to an atlas parcel:
-L <labelfile atlas_gcsa_file label_name>
Specify a manual label to align with atlas label <label name>
in the past I have used this to draw a central sulcus and force it to align
using the Destrieux atlas (since Desikan/Killiany is gyral). There are some
very nice tools in freeview that make this pretty trivial. Overlay sulc on
the inflated surface, make sure that the dark gray of the central sulcus
(or red) isn't connected to anything else. If it is make a line using the
custom fill tool, then fill and save. Once you are familiar with the tools
it will take you about 60 seconds
cheers
Bruce
On Fri, 13 Mar 2020,
Fraser Smith wrote:
>
> External Email - Use Caution
>
> Hi there
>
> I have a clear parcellation error with one participant who does look to have
> an atypical structure around the right post-central gyrus (looks split in
> two).
>
> Both the pre and post central gyri are shifted significantly backwards – but
> only for the right not the left hemisphere.
>
> I see this has been mentioned before in the archives – but I have been
> unable to find a fix for this.
>
> Could you provide any tips on what to try? I am using v6.0.0.
>
> Best wishes
>
> Fraser Smith
>
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1Q3tNsx2i8S7u3rTrRg5kVkRbFaZIpG8ua68_LGfivdEgkpw5ajZkBI2qAfAW6x_WW3NmJF7ezbi8vamEMqg2BsJToJHTJzM-bWG7gPpnUzW8QFFwSlGdaxz9NKnWFVK2QSLWaoNNZjNoWGVDi15vQiackvItyGkj0LGM-4q9FVnua7TtVkweDmYYlFm05uM5vPf4fucRlQ8zE67WvjXc9Bc-yBCjtmGWSgpf_G3lwWD6xuJyM4oAuBab27AQ9JhEB9Q_9ofAcplsumOf66ORZQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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 http://www.massgeneralbrigham.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.
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.
