AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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July 17, 2014 11:23AM
Hi AFNI experts,

We run our own bias field correction on the anatomical scans. I use these corrected scans for the afni_proc script and run into the following error.
3dSeg -anat anat_final.001+orig -mask AUTO -classes CSF ; GM ; WM
++     Notice SUMA_estimate_bias_field_Wells (SUMA_SegFunc.c:4713 @16:14:17):
Debug or NAN for voxel 4145 [92 21 0]
Cls CSF, M nan, S nan, Ai 100.689583 (fAset=0.014080 * 7151)
Gik 0.999664, Ri nan, sdf nan
--     Error SUMA_estimate_bias_field_Wells (SUMA_SegFunc.c:4718):
Have NAN, will return
--     Error SUMA_SegEngine (SUMA_3dSeg.c:506):
Failed to estimate bias
--     Error 3dSeg (SUMA_3dSeg.c:929):
Failed in SUMA_SegEngine

Is there an option to switch off bias field correction in the mask block of the afni_proc script?

Best wishes

Michael M
Subject Author Posted

3dSeg error on bias field corrected MPRAGEs

meinternational July 17, 2014 11:23AM

Re: 3dSeg error on bias field corrected MPRAGEs

rick reynolds July 18, 2014 03:20PM