Dear freesurfer developers,
I call recon-all -all from a matlab script using a system(cmd) which is (apparently) correctly executed, as shown in the recon-all.log (matlab_* attached), i.e.:
/usr/local/freesurfer/bin/recon-all -all -cw256 -3T -multistrip -clean-bm -i /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s /home/gc/study/recon-all/400614dclass
and apparently it run without errors as you can see in the matlab_recon-all.log file, but I get (systematically) a wrong
TalAviQA: 0.00000
while, if I run the above bash command directly I get a correct:
TalAviQA: 0.97713
as shown in the bash_recon-all.log (attached). I guessed that something wrong happened in
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig
and the error traced in talairach_avi.log (matlab_* and bash_* attached). In fact matlab_talairach_avi.log is shorter and all imgreg_4dfp end sections are missing which imply that TalAviQA can not be extracted by awk and mritotal transform is performed instead. But really I don't understand why this happens and whether similar issues affects other recon-all subtask using matlab. I double checked this on two linux sistems and with fs version 6.0 and 5.3 ... same results.
Thanks in advance for any help,
cheers,