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Freesurfer experts,
I'm having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces.
The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration.
The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature maps they look in alignment prior to registration, but using this unregistered sphere still puts the labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn't shown in freeview.
Please advise,
Chris.
Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au www.mcri.edu.auhttp://www.mcri.edu.au/
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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Hi Chris
you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful
cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote:
External Email - Use Caution
Freesurfer experts,
I’m having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces.
The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration.
The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature maps they look in alignment prior to registration, but using this unregistered sphere still puts the labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn’t shown in freeview.
Please advise,
Chris.
Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au
www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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External Email - Use Caution
Thanks Bruce.
I had to increase the angular search range in the affine part to get it to work.
Cheers,
Chris.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_register problem
Hi Chris
you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful
cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote:
External Email - Use CautionFreesurfer experts,
I'm having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces.
The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration.
The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature maps they look in alignment prior to registration, but using this unregistered sphere still puts the labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn't shown in freeview.
Please advise,
Chris.
Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au
www.mcri.edu.auhttp://www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
P Please consider the environment before printing this email
Disclaimer
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
how much? Maybe we should expand the default range? I thought it was already pretty broad, but I haven't looked at it in a long time Glad to hear it worked out cheers Bruce On Tue, 18 Sep 2018, Chris Adamson wrote:
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Thanks Bruce.
I had to increase the angular search range in the affine part to get it to work.
Cheers,
Chris.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_register problem
Hi Chris
you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful
cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote:
External Email - Use Caution
Freesurfer experts,
I’m having an issue with projecting labels from an atlas to a subject. I have a static annot file
on
the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register
my
subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces.
The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration.
The strange thing is that when I view the spherical surfaces in freeview with the overlaid
curvature
maps they look in alignment prior to registration, but using this unregistered sphere still puts
the
labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn’t shown in freeview.
Please advise,
Chris.
Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au
www.mcri.edu.au
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise
deal
with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from
or
in respect of the Communication.
P Please consider the environment before printing this email
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chris Adamson