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 > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>> -- > >>>> 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/ > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> The information in this e-mail is intended only for the person to whom > >>>> it is > >>>> addressed. If you believe this e-mail was sent to you in error and the > >>>> e-mail > >>>> contains patient information, please contact the Partners Compliance > >>>> HelpLine at > >>>> http://www.partners.org/complianceline . If the e-mail was sent to you > >>>> in error > >>>> but does not contain patient information, please contact the sender and > >>>> properly > >>>> dispose of the e-mail. > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer