Dear all,
I have come up with a pretty good preliminary solution namely:
I run the first loop that returns me CNR and some other stuff from the command
mri_cnr. It creates one txt. file for each subject.
for i in *3T; do mri_cnr $i/surf $i/mri/norm.mgz > $i/"$i"_cnr.txt; done
(All of my subjects' names contain the expression 3T, so if someone would like
to use it, just adjust it properly)
The second loop gives me a single txt. file with the list of cnr value only
(that is 'total CNR'). However, without subjects ID. I couldnt figure it out
yet, how to do this.
for i in $(find . -name *cnr.txt); do awk 'NR==8 {print $4}' "$i" >>
cnr_sample.txt; done
But all in all, I would say the problem is more or less solved, so thanks
everybody for your input.
Cheers,
Jacek
> gray/white CNR is the first column
> On Thu, 22 Jan 2015, Jacek Manko wrote:
>
> > 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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> >>
> >> --
> >> 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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> >
> >
> >
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