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  

Previous Message Next Message
Message List New Topic Print View
|
Zhihao Li
June 20, 2013 11:01AM
Hi AFNI experts,
I was running align_epi_anat.py, but the script halted with a message saying

3dSkullStrip -orig_vol -input ./__tt_filename.nii.gz -prefix ./__tt_filename.nii.gz_ns
** ERROR: Could not strip skull
** ERROR - script failed

However, the outputs of __tt_filename.nii.gz_ns+orig.* have already been generated and they are fine based on my visual inspection.
I also tried @NoisySkullStrip -input ./__tt_filename.nii.gz. It ran and completed without any error, and the output looks extremely similiar to the output of 3dSkullStrip.

So here I am satisfied with the outputs of both 3dSkullStrip and @NoisySkullStrip, but the 3dSkullStrip breaks the script pipeline of align_epi_anat.py for unknown reason. I am wondering how can I opt to use @NoisySkullStrip in align_epi_anat.py so it won't break and finish the alignment of anat-to-epi.
Reply Quote
RSS
Subject Author Posted

opt to use @NoisySkullStrip in align_epi_anat.py?

Zhihao Li June 20, 2013 11:01AM

Re: opt to use @NoisySkullStrip in align_epi_anat.py?

Rob June 25, 2013 06:20PM

Re: opt to use @NoisySkullStrip in align_epi_anat.py?

Daniel Glen June 26, 2013 03:53PM