Dear Dr. Greve, dear Dr. Fischl

> would something like this work?
> 
> set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf 
> $SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
> echo $subject $cnr > yourfile

Unfortunately it doesnt. I was trying to modify the paths, but got always 
results like: 

MRISread(/surf/lh.white): could not open file
No such file or directory
mri_cnr: could not read surface file /surf/lh.white
No such file or directory

and @Dr. Fischl

> actually if you run mri_cnr with -l out.log it will write a line to 
> out.log
> of the form:
> 
> gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean 
> sqrt(white_var) sqrt(gray_var) sqrt(csf_var))
> 
> 
> so you would create one file for each subject. You could then run a for
> loop over your subjects to cat them into a single file
> 


Indeed, but I dont quite get it, how to extract CNR from these values.


Thanks,


Cheers,
Jacek Manko

> On 01/21/2015 02:46 PM, Jacek Manko wrote:
> > My desirable output would be then a .txt file that consists of merely 
> two columns. The first column is the subject's ID and the second is the 
> CNR value only, for example:
> >
> > bruce 1.602
> > bert 1.555
> > john_doe 1.666
> >
> > Thanks in advance.
> >
> > Cheers,
> > Jacek
> >
> > Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
> >> Hi Jacek
> >>
> >> if you give us an example of what the desired output would be for you it
> >> would just be a couple of minutes to put it in the code. Or maybe someone
> >> can post some sed code (or some easy alternative) to parse the CNR out of
> >> the output.
> >>
> >> Bruce
> >>
> >>
> >> On Wed,
> >> 21 Jan 2015, Jacek Manko wrote:
> >>
> >>> Oh, I thought it was already defined. I am referring actually to this
> >> thread...
> >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
> >>>
> >>> ...and, allowing myself to specify my problem, when I type the command
> >> 'mri_cnr' what I become in my terminal is something more or less like
> >> that:
> >>> "
> >>>>> 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
> >>> "
> >>>
> >>> My question is, if there is a way to export the CNR value, that is
> >> 1.602, to a seperate file alongside with the subject's ID. I suppose
> >> there are no such bulit-in commands in FreeSurfer, is that right?
> >>> Thanks.
> >>>
> >>>
> >>> Cheers,
> >>> Jacek Manko
> >>>
> >>>
> >>>
> >>> Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
> >>>> how do you want to define CNR?
> >>>>
> >>>> On 01/21/2015 06:21 AM, Jacek Manko wrote:
> >>>>> Dear All,
> >>>>>
> >>>>> I have been wondering if there is a way (already implemented in the
> >>>> FreeSurfer) to export CNR measurement outputs to seperate file, like a
> >>>> table or someting. If not, it will possible only via some pretty
> >>>> advanced bash scripting, am I right? If so, has anyone some experience
> >>>> with that matter?
> >>>>> Thanks.
> >>>>>
> >>>>> Cheers,
> >>>>> Jacek Manko
> >>>>>
> >>>>>
> >>>>> _______________________________________________
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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
> >>>>
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> >>>>
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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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