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Freesurfer,
Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz?
Thank you,
Chris.
Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT)
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/
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Hi Chris
can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote:
External Email - Use Caution
Freesurfer,
Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz?
Thank you,
Chris.
Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
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 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.
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So all voxels in the brainmask that are non-zero are in the brain mask? In other words zero-valued voxels in the brain are considered to be non-brain?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, 27 August 2019 12:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] binary version of brainmask?
Hi Chris
can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote:
External Email - Use CautionFreesurfer,
Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz?
Thank you,
Chris.
Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
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 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.
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.
Yes, although I think we use a threshold of 5 not 0 Cheers Bruce
On Aug 26, 2019, at 10:24 PM, Chris Adamson chris.adamson@mcri.edu.au wrote:
External Email - Use CautionSo all voxels in the brainmask that are non-zero are in the brain mask? In other words zero-valued voxels in the brain are considered to be non-brain?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, 27 August 2019 12:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] binary version of brainmask?
Hi Chris
can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote:
External Email - Use CautionFreesurfer,
Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz?
Thank you,
Chris.
Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
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 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.
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.
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External Email - Use Caution
Thank you.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, 27 August 2019 12:28 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] binary version of brainmask?
Yes, although I think we use a threshold of 5 not 0 Cheers Bruce
On Aug 26, 2019, at 10:24 PM, Chris Adamson <chris.adamson@mcri.edu.aumailto:chris.adamson@mcri.edu.au> wrote:
External Email - Use Caution So all voxels in the brainmask that are non-zero are in the brain mask? In other words zero-valued voxels in the brain are considered to be non-brain?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Tuesday, 27 August 2019 12:18 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] binary version of brainmask?
Hi Chris
can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote:
External Email - Use CautionFreesurfer,
Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz?
Thank you,
Chris.
Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
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 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.
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 mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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