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

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jbcocjin
September 13, 2017 05:08PM
Hi AFNI experts -

We're trying to skull strip mouse and rat brains from T2 anatomicals. We noticed that, in 3dSkullStrip, there is a '-rat' option in the code. We tried the following command: 
3dSkullStrip -input T2.nii.gz -rat
but received the error: 
oo     Warning 3dSkullStrip (SUMA_3dSkullStrip.c:1565):
Input dataset has a very low value range.
If stripping fails, repeat with option -fac 1000
So, we tried: 
3dSkullStrip -input T2.nii.gz -rat -fac 1000
And received: 
Fatal Signal 11 (SIGSEGV) received
   THD_dset_scale
  3dSkullStrip
 Bottom of Debug Stack
** AFNI version = AFNI_17.1.12  Compile date = Jun 24 2017
** [[Precompiled binary linux_ubuntu_16_64: Jun 24 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=94 bytes=345102
** Crash log is appended to file /home/shah/.afni.crashlog

We're not sure what this erorr means and where to go from here. Your help would be much appreciated!

Cheers,
John and Shahab
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Subject Author Posted

Rodent skull stripping

jbcocjin September 13, 2017 05:08PM

Re: Rodent skull stripping

Daniel Glen September 14, 2017 01:59PM

Re: Rodent skull stripping Attachments

jbcocjin September 15, 2017 12:46PM

Re: Rodent skull stripping

Daniel Glen September 19, 2017 11:18AM