Thanks Doug!

On Mon, Feb 24, 2014 at 7:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

Use --seg instead of --mask. Also, use --id 1 to get only the ROI in the mask (otherwise it will give you the mask as one ROI and everything outside of the mask as a 2nd ROI)

doug

On 02/24/2014 12:51 PM, Garikoitz Lerma-Usabiaga wrote:

...

Hi, I have some volume ROIs in diffusion space (1-s and 0-s). I would like to obtain, for example, the average FA values in that ROI.

I tried using mri_segstats, but it gives me an error, it needs a segmentation volume. mri_segstats --i dmri/dtifit_FA.nii.gz --mask FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz --sum fa.stats

If I substitute --i for --seg I obtain a different error.

Which command should I use? I tried dmri_pathstats but it is asking for the file length.samples.txt, which I don't have and don't know how to generate.

thanks! Gari

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