thanks Dr. B.....that helped a lot
----- Original Message -----
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Kushal Kapse" <kka...@mail.med.upenn.edu>
Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, June 18, 2012 2:27:29 PM
Subject: Re: [Freesurfer] mri_cnr
Hi KK
this is something i wrote for myself, but you are welcome to try it out.
YOu don't need to give it the slope stuff, that is optional. The "vol"
command line parms are the volumes that you want to assess CNR in. For
example:
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz
processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
gray/white CNR = 2.241, gray/csf CNR = 1.026
lh CNR = 1.633
white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
gray/white CNR = 2.205, gray/csf CNR = 0.937
rh CNR = 1.571
total CNR = 1.602
On Mon,
18 Jun 2012, Kushal Kapse wrote:
> hi fellas,
>
> i am trying to run mri_cnr command in freesurfer to compute and see CNR for
> gray/white/csf.... the command gives following info as help:
>
> -bash-3.2$ mri_cnr
> usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ...
> -s <slope fname> <dist in> <dist out> <step in> <step out>
>
>
> i understand that 'surf directory'= subjects 'surf' folder ; but i am not
> able to figure out what it means by vol1, vol2 and slope fname......it doesnt
> show any error but just doesnt do anything even if i mention the surf
> directory to this command.....
>
> i checked on freesurfer mail archive, but no info since 2009 about any update
> on this command.....
>
> may someone please give an info if anyone ever used this command
>
>
> thanks
> kk
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>
>
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