Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
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Thank you.
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I did:
mris_inflate -n 5 wmparc.mgz inflateTest.mgz
I wasn't sure oh what my input file should be. It resulted in the following message:
No such file or directory freadFloat: fread failed
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, March 1, 2017 11:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
yea, you have to run it on a surface, usually the white, eg,
mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna
On 03/01/2017 11:45 AM, Crawford, Anna wrote:
I did:
mris_inflate -n 5 wmparc.mgz inflateTest.mgz
I wasn't sure oh what my input file should be. It resulted in the following message:
No such file or directory freadFloat: fread failed
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, March 1, 2017 11:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Got it! Thank you,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, March 1, 2017 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume
yea, you have to run it on a surface, usually the white, eg,
mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna
On 03/01/2017 11:45 AM, Crawford, Anna wrote:
I did:
mris_inflate -n 5 wmparc.mgz inflateTest.mgz
I wasn't sure oh what my input file should be. It resulted in the following message:
No such file or directory freadFloat: fread failed
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, March 1, 2017 11:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Hi Anna
yes, if you reduce the number of iterations it will inflate less. For example, from the surf dir:
mris_inflate -n 1 ./lh.smoothwm ./lh.smoothwm.n1
will generate a slightly inflated surface
cheers Bruce
On Wed, 1 Mar 2017, Crawford, Anna wrote:
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this?
Thanks,
Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Crawford, Anna -
Douglas N Greve