[Freesurfer] mri_cnr and bash

matter? Thanks. Cheers, Jacek Manko ___ 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

Re: [Freesurfer] mri_cnr and bash

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

Re: [Freesurfer] mri_cnr and bash

ruce > > > 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, allow

Re: [Freesurfer] mri_cnr and bash

ndeed, 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 se

Re: [Freesurfer] mri_cnr and bash

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,

Re: [Freesurfer] QA measures

You may find this paper useful: http://www.biomedcentral.com/1471-2342/12/27 Authors describe there some measures such as "Euler number" and “Contrast to Noise ratio (CNR)". Actually, they dont belong to QA package, but they are definitely worth looking at. Best, Jacek Manko

Re: [Freesurfer] QA measures mgz

; > Message: 1 > Date: Fri, 17 Jul 2015 18:24:28 +0200 > From: "Jacek Manko" > Subject: Re: [Freesurfer] QA measures > To: Freesurfer support list > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: <55a92c3ce71501.52368...@wp.pl> > Content-Type: te

[Freesurfer] Cortical parcellation and mri_annotation2label

mri_annotation2label, I got different labels than those mentioned before. My question therefore is, what can be consider as a output of cortical parcellation procedure, i.e. when I am about to pick some cortical seeds for further analyses? Kind regards, Jacek Manko

Re: [Freesurfer] TRACULA messy tracts

lopment version of freesurfer. The 5.3 version doesn't have the > capability to read these tables from the dicoms but the 6.0 version will. > In the meantime you can download the dev version and use mri_convert from > that version. > > Best, > > a.y > > On Su

[Freesurfer] TRACULA and NIFTI images

clueless on what that might be. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=3xql45jb18z Is there anything you could advise me on? Thanks in advance. Best, Jacek Manko Dnia 7-03-2016 o godz. 21:17 Anastasia Yendiki napisał(a): > Hi Jacek - I'm attaching the files. > > a.y >