Merci bien :). On Wed, Feb 18, 2015 at 2:54 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote:
> > Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats, > because that will give you a robust maximum (i.e., if there are a couple of > voxels that are outliers with a very high value it won't take them into > account, which is probably a good idea here). Then use 20% of that robust > maximum as your lower threshold and voila, you have your ROI. > > Best, > a.y > > > On Wed, 18 Feb 2015, Barbara Kreilkamp wrote: > > 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 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-mai >> l >> contains patient information, please contact the Partners Compliance >> HelpLin >> e at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in er >> ror >> but does not contain patient information, please contact the sender and >> prop >> erly >> dispose of the e-mail. >> >> >> >> >> > _______________________________________________ > 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. > >
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