Thanks Douglas for your reply.
I checked in detail the talairach_avi.log files and they show that imgreg_4dfp c executable:
$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
are executed in both environment (bash and matlab), but in bash imgreg_4dfp call in turn
$Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $
that show eta,q values in the talairach_avi.log file. Seems to me that, if I call recon-all from matlab, fimgreg code ( which I don't know where it is) is not executed or it don't write results to talairach_avi.log output, but probably talairach avi transform is fine.
... very strange behaviour.
Cheers,
Giuseppe
On 11/09/2017 18:25, Douglas N Greve wrote:
The tal_QC_AZS scripts expects the log file to have a specific format, and it looks like something changes when you run it inside matlab. sorry, the only idea I have is that the linux environments might be different in bash vs matlab.
On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
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,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer