Hi Lily - No, you should search for dmri_pathstats in the log file (scripts/trac-all.log) and follow the syntax for the command that you'll see there. Only change the threshold, and potentially the output file, if you don't want to overwrite the existing one.

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Lily LWANG49@partners.org Sent: Friday, March 13, 2020 3:50 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] dmri_pathstats segment

Hi,

I am trying to get voxel by voxel stats for fmajor on a threshold that's not the 0.2 default because when I looked at merged nii, fmajor is constructed correctly but on a different threshold. This is the command I used:

dmri_pathstats --intrk fmajor_PP_avg33_mni_bbr/path.pd.trk --dtbase ../dmri/dtifit --outvox new_fmajor --pthr 0.4

And I am getting in the terminal:

INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 940 streamlines as length outliers INFO: Have 1460 total streamlines (min/mean/max length: 75/101/117) INFO: Have 1460 non-truncated streamlines (min/mean/max length: 75/101/117) Segmentation fault (core dumped)

Am I running the command incorrectly?

Thank you, Lily