Thank you very much Anastasia, May I please check with you if what I am thinking of doing sounds correct? I would use fslstats in FSL with the flag -R which gives me the maximum value. For Forceps major I get a value of 200, 20% of this value would be 40, so then in the path.pd.nii.gz image I threshold every value below 40 away. Is it fine to use the -R flag in fslstats (I do not believe I should use the -r flag)?
Best wishes, Barbara Anne Usage: fslstats [-t] <input> [options] -t will give a separate output line for each 3D volume of a 4D timeseries Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean -l <lthresh> : set lower threshold -u <uthresh> : set upper threshold -r : output <robust min intensity> <robust max intensity> -R : output <min intensity> <max intensity> > > On 17/02/2015 14:47, Anastasia Yendiki wrote: > > > Hi Barbara Anne - In each tract's directory, you'll find the tract as a > volumetric probability distribution in the file path.pd.nii.gz. You can use > that as an ROI to extract statistics from any other volume that's in the > same space as the tracts (native DWI space). To be consistent with the FA, > MD, etc stats that are produced by default by trac-all, you'd threshold > path.pd.nii.gz to 20% of its max value before using it as an ROI. > > Hope this helps, > a.y > > On Mon, 16 Feb 2015, Barbara Kreilkamp wrote: > > Dear TRACULA experts, > > I wonder if you could please assist me in extracting tract values from an > image I > transferred to diffusion space. > > I ran TRACULA on my DTI dataset, however from other structural images I > aim to extract > values for tracts as well. > > I also extracted DTI derived measures from these tracts of my DTI data > (FA,MD,RD,AD), > using this command: trac-all -stat -c dmrirc > And now I wonder whether I could add another line to the source code of > the stats > command so that it would output values from that other image I have in > diffusion > space. > > Best wishes and thank you, > Barbara Anne > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > athttp://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. > > >
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