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