Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to "fix" it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards,
Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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.
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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.
I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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.
I see. Then why use our wrapper at all? Just convert to nifti and run N3 directly. On Tue, 24 Apr 2012, Popescu, V. wrote:
I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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.
I'll try that. Thank you!
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 16:24 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
I see. Then why use our wrapper at all? Just convert to nifti and run N3 directly. On Tue, 24 Apr 2012, Popescu, V. wrote:
I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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.
Hi Veronica,
If you still want to use mri_nu_correct.mni, but retain the original dimensions, you can include '--no-float' to the command line.
i.e,
mri_nu_correct.mni --i <input_vol> --o <output_vol> --no-float
That should solve the problem.
Regards, Sindhuja
I'll try that. Thank you!
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 16:24 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
I see. Then why use our wrapper at all? Just convert to nifti and run N3 directly. On Tue, 24 Apr 2012, Popescu, V. wrote:
I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much! It works now! Best regards, Veronica
-----Original Message----- From: Sindhuja Tirumalai Govindarajan [mailto:sindhuja@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 19:29 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica,
If you still want to use mri_nu_correct.mni, but retain the original dimensions, you can include '--no-float' to the command line.
i.e,
mri_nu_correct.mni --i <input_vol> --o <output_vol> --no-float
That should solve the problem.
Regards, Sindhuja
I'll try that. Thank you!
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 16:24 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
I see. Then why use our wrapper at all? Just convert to nifti and run N3 directly. On Tue, 24 Apr 2012, Popescu, V. wrote:
I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size
thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] mri_convert - returns different image size
Hi Veronica
can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do.
cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote:
Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to ?fix? it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Popescu, V. -
Sindhuja Tirumalai Govindarajan