Hi freesurfer team,
I collected an MPRAGE in Bay2 scanner (0.75 x 0.75 x 0.75 mm resolution), and the recon-all procedures with freesurfer version 6.0.0 and 7.1.1 were both failed. I'm not sure if this is due to the participant's large CSF or motion or something else.
I have attached the log files (recon-all.log and talairach.log from both versions), which I noticed a warning/error in the recon-all.log : (version6.0.0) WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
(version6.0.0 and 7.1.1) ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
mritotal -verbose -debug -clobber -modeldir /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7133/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg /usr/local/freesurfer/stable6_0_0/mni/share/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log
I have tested the recon-all with another Bay2 data (from different project in our group), and it worked perfectly (with version 6.0.0) with the same script. Thus, I did not think this is due to my script or FS version..
Thanks, Jeungchan