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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HShuaib
September 12, 2015 02:49PM
Hello,

I am trying to use the -use_skull option with 3dSkullStrip but it can't find the qhull command even though the binary is present in the same directory.

This is the output:

$ ./3dSkullStrip -input ../../../Development/brain/ATLAS/N4_DN_t1.head.nii.gz -prefix USE_SKULL_t1.head.nii -use_skull
sh: qhull: command not found
-- Error SUMA_q_wrap (SUMA_GeomComp.c:14577):
1st fscanf fails

Error SUMA_LoadPrepInVol:
Failed in SUMA_qhull_wrap

Fatal Signal 11 (SIGSEGV) received
SUMA_SkullMask
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = Aug 27 2015
** [[Precompiled binary macosx_10.7_Intel_64: Aug 27 2015]]
** 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.

Any ideas?

Many thanks.
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Subject Author Posted

qhull present but 3dSkullStrip can't find it.

HShuaib September 12, 2015 02:49PM

Re: qhull present but 3dSkullStrip can't find it.

rick reynolds September 13, 2015 02:39PM