Re: [Freesurfer] mri_binarize --gm

[Douglas Greve]

try making it executable,

chmod a+x mri_binarize

then run rehash and see if it work


On 2/24/17 12:13 AM, Jinsong Tang wrote:

Dear all,

I am trying to run a mri_binarize command on FS 5.3

   mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz
   I obtain this:
ERROR: Option –gm unknown

I found there was a previous post suggest to use the new mri_binarize from
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize

I download this one, and replace the old one with this new one.

however, I obtian this:
mri_binarize : command  not found.

How to fix this?

Thanks and best,

Jinsong


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Re: [Freesurfer] mri_binarize --gm

[Jinsong Tang]

Hello.

I have installed the new version of mri_binarize.
However, I got a new problem.

--
GNU libc version: 2.19
ERROR: Systems running GNU glibc version greater than 2.15
  require a newly formatted license file (it's free). Please
  download a new one from the following page:
  http://surfer.nmr.mgh.harvard.edu/registration.html

I download a new license. But I still keep getting this error message.

Thanks,

Jinsong

On Thu, Feb 23, 2017 at 9:13 PM, Jinsong Tang 
wrote:

> Dear all,
>
> I am trying to run a mri_binarize command on FS 5.3
>
>   mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz
>   I obtain this:
>ERROR: Option –gm unknown
>
> I found there was a previous post suggest to use the new mri_binarize from
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
>
> I download this one, and replace the old one with this new one.
>
> however, I obtian this:
>
> mri_binarize : command  not found.
>
> How to fix this?
>
> Thanks and best,
>
> Jinsong
>
>


-- 
Jinsong Tang, MD
Institute of Mental Health
The Second Xiangya Hospital , Central South University
139 Renmin Road, Changsha Hunan 410011, P.R. China
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[Freesurfer] mri_binarize --gm

[Jinsong Tang]

Dear all,

I am trying to run a mri_binarize command on FS 5.3

  mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz
  I obtain this:
   ERROR: Option –gm unknown

I found there was a previous post suggest to use the new mri_binarize from

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize

I download this one, and replace the old one with this new one.

however, I obtian this:

mri_binarize : command  not found.

How to fix this?

Thanks and best,

Jinsong
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Re: [Freesurfer] mri_binarize --gm option unknown

[Douglas N Greve]

try this version

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize

On 11/02/2016 12:37 PM, HOSSU Gabriela wrote:
>
> Hello everyone,
>
> I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, 
> but when I use the option —gm (also for –subcort-gm).
>
> I am getting an error that says the —gm option is not recognized.
>
> Here is the command line and the following error (from the mri folder 
> of a subject):
>
> mri_binarize –i aparc+aseg.mgz –gm –o gmmask.mgz
>
> I obtain this:
>
> ERROR: Option –gm unknown
>
> Thanks very much,
>
> Gabriela HOSSU
>
>
>
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-- 
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/

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[Freesurfer] mri_binarize --gm option unknown

[HOSSU Gabriela]

Hello everyone,

I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, but when I 
use the option -gm (also for -subcort-gm).
I am getting an error that says the -gm option is not recognized.

Here is the command line and the following error (from the mri folder of a 
subject):
mri_binarize -i aparc+aseg.mgz -gm -o gmmask.mgz

I obtain this:
ERROR: Option -gm unknown

Thanks very much,

Gabriela HOSSU

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