Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards,Vilde
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe
cheers Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 .
I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command :
recon-all -s [subject] -i T1.nii -i flair.nii -all
Kind regards, Vilde
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be?
Best, Vilde
Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe
cheers Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 .
I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command :
recon-all -s [subject] -i T1.nii -i flair.nii -all
Kind regards, Vilde
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you would have to first run recon-all -all on the T1 On Wed, 8 Oct 2014, Vilde wrote:
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be?
Best, Vilde
Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe
cheers Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 .
I read in the release notes that in version 5.2 you can use the flag -FLAI
R
when you are using a flair image as input. I suppose this will not run in
an
earlier version? Would it be correct to use the following command :
recon-all -s [subject] -i T1.nii -i flair.nii -all
Kind regards, Vilde
_______________________________________________ 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.
I will try that.
Have a good day!
Date: Wed, 8 Oct 2014 14:07:38 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
you would have to first run recon-all -all on the T1 On Wed, 8 Oct 2014, Vilde wrote:
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be?
Best, Vilde
Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe
cheers Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 .
I read in the release notes that in version 5.2 you can use the flag -FLAI
R
when you are using a flair image as input. I suppose this will not run in
an
earlier version? Would it be correct to use the following command :
recon-all -s [subject] -i T1.nii -i flair.nii -all
Kind regards, Vilde
_______________________________________________ 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 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Vilde