RE: Surface Based Analysis - Setup Error (??)

[color=#000000]Hi Shady,[/color]

[color=#000000]Yes, I think so. This error message means that the white matter mask for that subject was empty, again indicating (assuming that the gray/white/csf masks had been imported from the freesurfer folders for your subjects) that freesurfer might have run through some issues with the registration and/or segmentation of this subject data, so I would probably suggest to re-run recon-all and visually inspect the results to make sure that everything looks fine. [/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Shady El Damaty:[/i][quote]Thanks Alfonso,

I will try rerunning this subject again with recon-all.  After excluding this subject, I noticed the following error when processing my ROIs:

ERROR DESCRIPTION:[quote]
Error using conn_process (line 597)
No suprathreshold voxels in ROI file /Volumes/Archive/Research/ADS/data/ads.subjects/402568-w1/mri/c2brainmask.nii (this typically indicates a problem during normalization/segmentation for this subject; please try re-running normalization/segmentation step after manually re-aligning the structural volumes to better match the default template orientation)
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools
Matlab v.2015b
storage: 2968.7Gb available
[/quote]Is this a related problem, probably due to copying files?  I can probably just rerun recon-all and it should be fine?[/quote]