Hello Freesurfer developers,
I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction.
1) Freesurfer version: 6.0.0
If you want to just run the recon-all pipeline without using n3, you'll have to do something else. You can copy orig.mgz to nu.mgz (or create a symbolic link, which is probably better), then run with -nonuintensitycor
On 1/29/18 7:14 PM, Alexis Moscoso wrote:
Hello Freesurfer developers,
I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction.
- Freesurfer version: 6.0.0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Douglas. Just one more quick question: will -nonuintensitycor work if I set the -3T flag? As far as I know, -3T changes some parameters of the N3 correction and makes use of Schwarz atlas. I was wondering whether this flag interferes with -nonuintensitycor.
El El sáb, 3 feb 2018 a las 21:01, Douglas Greve greve@nmr.mgh.harvard.edu escribió:
If you want to just run the recon-all pipeline without using n3, you'll have to do something else. You can copy orig.mgz to nu.mgz (or create a symbolic link, which is probably better), then run with -nonuintensitycor
On 1/29/18 7:14 PM, Alexis Moscoso wrote:
Hello Freesurfer developers,
I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction.
- Freesurfer version: 6.0.0
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I don't think so
On 2/3/18 3:28 PM, Alexis Moscoso wrote:
Thanks Douglas. Just one more quick question: will -nonuintensitycor work if I set the -3T flag? As far as I know, -3T changes some parameters of the N3 correction and makes use of Schwarz atlas. I was wondering whether this flag interferes with -nonuintensitycor.
El El sáb, 3 feb 2018 a las 21:01, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> escribió:
If you want to just run the recon-all pipeline without using n3, you'll have to do something else. You can copy orig.mgz to nu.mgz (or create a symbolic link, which is probably better), then run with -nonuintensitycor On 1/29/18 7:14 PM, Alexis Moscoso wrote:Hello Freesurfer developers, I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction. 1) Freesurfer version: 6.0.0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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Douglas Greve