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
Did you check the transform? It was the automatic failure detection that threw the error. This can sometimes happen when the head is at a "funny" orientation in the scanner, but at 7T there might be some bias fields having an effect. Also, see if it works when you sample it at 1mm (just don't use the -hires option to recon-all).
On 4/7/2022 12:17 PM, Lee, Jeungchan wrote:
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
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Lee, Jeungchan