External Email - Use Caution
Hello Randy, I think the expectation is for users to run “samseg” from the command line. (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can’t speak to the validity of the command + options causing the crash, but I would look too see if a “core” file was written in the directory where the command ran that produced the “Illegal instruction” error and subsequent crash. The core file might also be under /var/crash. If you have the core file you could name it something unique and try uploading it to https://secure-web.cisco.com/13zdjoSMY5sCPpxW673b6aDxUESbBUC7j-BF_Pk3NBIpXnw... someone to look at. - R.
On Feb 24, 2022, at 11:58, daedalus39@aol.com wrote: External Email - Use Caution Following up on yesterday's email:I looked up the help text for SAMSEG on the VM (“run_samseg –help”). The flag for --lesion indicates that Tensorflow is required. --lesion Enable lesion segmentation (requires tensorflow). I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing. While my question only reported the “core dump” and a request to check the syntax, I did ask if the “lesion” flag was implemented in the VM. If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it?Sincerely,-Randy-----Original Message-----From: daedalus39@aol.comTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Sent: Wed, Feb 23, 2022 1:19 pmSubject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67Dear Experts,I am trying to test SAMSEG "lesion" on VM_67 and after I entered:run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/...I got the following errorIllegal instruction (core dumped)Is there anything glaringly wrong in my instruction/input phrase?Is SAMSEG "lesion" implemented in the new VM? I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine)Thanks in advance for any help.-Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer