Hallo, first of all: Sorry to be a little bit clingy, but I have some problems in understanding regarding the DIAG option in FreeSurfer. As suggested by Bruce, I have set DIAG to 0xFFFFFFFF and DIAG_VERBOSE to 1. I am getting a lot of output now and a very large recon-all.log.
Unfortunately, I am not able to run a recon-all on the OASIS-Brains subject "OAS1_0001_MR1" and "OAS1_0004_MR1" successfully after converting the *.img to *.mgz via mri_convert.
I order to get FreeSurfer in the cloud, I have created a minimum archive of FreeSurfer 6.0.0 using strace to monitor all files that are being accessed in the course of recon-all. The archive does not seem to work with DIAG set to 0xFFFFFFFF.
I am not sure, but my first guess is that the DIAG option also influences the recon-all pipeline. Is this right? Is there a way to increase the log level without influecing any analysis steps? The whole run takes much longer than a "normal" recon-all without DIAG set to any level. My current run fails with:
... HIPS unsupported No such file or directory Linux neuroimaging02 4.8.0-53-generic #56~16.04.1-Ubuntu SMP Tue May 16 01:18:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s OAS1_0001_MR1 exited with ERRORS at Wed May 31 02:54:32 UTC 2017
I will prepare a new run with strace and the original FreeSurfer-archive to check process behavior when DIAG is set to 0xFFFFFFFF. Unfortunately, everything takes so much time...
I have a prepared a large test scenario with different hardware constellations to check if the encountered SegFault is hardware on not software related.
Thank you very much!
Regards, Jens