Re: [Freesurfer] FNIRT all NaN's
Sent this to the wrong list. Apologies. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 From: Funk, Quentin Sent: Wednesday, February 8, 2017 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: FNIRT all NaN's Freesurfer experts, I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs. I ran the program in verbose mode--and everything is NaN's. e.g.: SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan Jacobian range is nan -- nan ***Going to next resolution level*** Setting subsampling Setting reg mode Setting lambda New Lambda: 30 SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan Is this simply because there are NaN's in the input image? Will replacing them with 0 fix the issue, or will it lead to strange behaviour in FNIRT? Any help is appreciated. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. ___ 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.
Re: [Freesurfer] FNIRT all NaN's
Shouldn't you post this to the FSL list? On 02/08/2017 12:17 PM, Funk, Quentin wrote: > > Freesurfer experts, > > > I have a few fractional anisotropy images linearly registered to an FA > atlas. I'd like to run FNIRT on them with reference the FA Atlas, but > when I do, the output is entirely NaNs. > > > I ran the program in verbose mode--and everything is NaN's. e.g.: > > > SSD = -nann = 0Disp reg = nanInt reg = -nan Total Cost = nan > Jacobian range is nan -- nan > ***Going to next resolution level*** > Setting subsampling > Setting reg mode > Setting lambda > New Lambda: 30 > SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost > = nan > SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost > = nan > SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost > = nan > SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost > = nan > > > Is this simply because there are NaN's in the input image? Will > replacing them with 0 fix the issue, or will it lead to strange > behaviour in FNIRT? > > > Any help is appreciated. > > > Quentin Funk, PhD > Houston Methodist Research Institute > 713-363-9003 > > Houston Methodist. Leading Medicine. > > /U.S. News & World Report/ has recognized Houston Methodist as one of > the nation’s top 20 hospitals, placing it for the second time on the > magazine’s prestigious Honor Roll. It is also designated as a Magnet > hospital for excellence in nursing. Visit us at houstonmethodist.org > . Follow us at twitter.com/MethodistHosp > and facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist and/or its relevant affiliates and may contain restricted > and privileged material for the sole use of the intended recipient(s). > Any review, use, distribution or disclosure by others is strictly > prohibited. If you are not the intended recipient (or authorized to > receive for the recipient), please contact the sender and delete all > copies of the message. 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 gr...@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.
[Freesurfer] FNIRT all NaN's
Freesurfer experts, I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs. I ran the program in verbose mode--and everything is NaN's. e.g.: SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan Jacobian range is nan -- nan ***Going to next resolution level*** Setting subsampling Setting reg mode Setting lambda New Lambda: 30 SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan Is this simply because there are NaN's in the input image? Will replacing them with 0 fix the issue, or will it lead to strange behaviour in FNIRT? Any help is appreciated. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. ___ 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.
