Hi Doug, I would like to inquire about the command " mri_binarize". In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz .... etc without the need to convert the output "mgz" files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:
mri_binarize --i aseg.mgz --o precentral.nii --match 1024
The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output "mgz" then convert it to nifti!!
Is this real or I am missing something? Thanks for any advice!
By the way I see this issue came up recently and in both freesurfer V 5.3 and V6
Best, Mohamad
Hi Mohamad
can you send us the command lines and screen outputs from doing it both ways? The output format shouldn't change things - there is no reason you shouldn't be able to write directly to nifti
cheers Bruce
On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote:
Hi Doug,
I would like to inquire about the command “ mri_binarize”. In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz …. etc without the need to convert the output “mgz” files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:
mri_binarize --i aseg.mgz --o precentral.nii --match 1024
The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output “mgz” then convert it to nifti!!
Is this real or I am missing something? Thanks for any advice!
By the way I see this issue came up recently and in both freesurfer V 5.3 and V6
Best,
Mohamad
Thanks Bruce for the quick response! I finally found what is going on. Actually the input file for 6 of my subjects is badly segmented so I guess that it return empty due to missing labels!
Sorry for the confusion and thanks again
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, March 12, 2016 4:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binarize
Hi Mohamad
can you send us the command lines and screen outputs from doing it both ways? The output format shouldn't change things - there is no reason you shouldn't be able to write directly to nifti
cheers Bruce
On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote:
Hi Doug,
I would like to inquire about the command “ mri_binarize”. In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz …. etc without the need to convert the output “mgz” files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:
mri_binarize --i aseg.mgz --o precentral.nii --match 1024
The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output “mgz” then convert it to nifti!!
Is this real or I am missing something? Thanks for any advice!
By the way I see this issue came up recently and in both freesurfer V 5.3 and V6
Best,
Mohamad
no worries. That makes more sense Bruce On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote:
Thanks Bruce for the quick response! I finally found what is going on. Actually the input file for 6 of my subjects is badly segmented so I guess that it return empty due to missing labels!
Sorry for the confusion and thanks again
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, March 12, 2016 4:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_binarize
Hi Mohamad
can you send us the command lines and screen outputs from doing it both ways? The output format shouldn't change things - there is no reason you shouldn't be able to write directly to nifti
cheers Bruce
On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote:
Hi Doug,
I would like to inquire about the command “ mri_binarize”. In the past, this command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz …. etc without the need to convert the output “mgz” files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:
mri_binarize --i aseg.mgz --o precentral.nii --match 1024
The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output “mgz” then convert it to nifti!!
Is this real or I am missing something? Thanks for any advice!
By the way I see this issue came up recently and in both freesurfer V 5.3 and V6
Best,
Mohamad
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mohamad, I don't know why that would be. Note that the aseg does not have individual cortical labels. You should use aparc+aseg.mgz
On 03/12/2016 04:19 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I would like to inquire about the command “ mri_binarize”. In the past, this command was able to create a _binarized nifti_ mask from aseg.mgz, wmparc.mgz …. etc without the need to convert the output “mgz” files to nifti. In other words If I want to create a mask for the precentral gyrus I was using the following:
mri_binarize --i aseg.mgz --o precentral.nii --match 1024
The command was able to create the mask and convert it to nifti file at once, but right now if the output is nifti file, it returns empty so I need to make the output “mgz” then convert it to nifti!!
Is this real or I am missing something? Thanks for any advice!
By the way I see this issue came up recently and in both freesurfer V 5.3 and V6
Best,
Mohamad
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alshikho, Mohamad J. -
Bruce Fischl -
Douglas N Greve