Hi Jens
we need more information if we are to help you. Can you send the recon-all.log? Or at least the bit that shows the command that fails onwards?
The DIAG stuff should not change recon-all, but of course it might and if so we will track it down and fix it
cheers Bruce
p.s. The HIPS warning just means it couldn't recognize an input file. We don't support HIPS after we transitioned to open source ages ago as their license wasn't compatible On Wed, 31 May 2017, Jens Offenbach wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer