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.com
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Sent: Wed, Feb 23, 2022 1:19 pm
Subject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67

Dear 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 error

Illegal 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