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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
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



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