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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maitra
March 25, 2015 04:02PM
Now to do some actual work after the installation..

it appears that I do not have a 3dSkullStrip: 

$align_epi_anat.py -anat Datasets/Imagination/MPRAGEco.nii.gz -epi Datasets/Imagination/Imagination.nii.gz -epi_base 5 -epi2anat
#++ align_epi_anat version: 1.50
#Script is running:
  3dAttribute DELTA Datasets/Imagination/Imagination.nii.gz
#Script is running:
  3dAttribute DELTA Datasets/Imagination/Imagination.nii.gz
#Script is running:
  3dAttribute DELTA Datasets/Imagination/MPRAGEco.nii.gz
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
  \rm -f ./__tt_Imagination*
#Script is running:
  \rm -f ./__tt_MPRAGEco*
#Script is running (command trimmed):
  3dcopy Datasets/Imagination/MPRAGEco.nii.gz ./__tt_MPRAGEco+orig
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 25 2015) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
  3dSkullStrip -orig_vol -input ./__tt_MPRAGEco+orig -prefix ./__tt_MPRAGEco_ns
/bin/sh: 3dSkullStrip: command not found
** ERROR: Could not strip skull

** ERROR - script failed

Why is 3dSkullStrip not created?

Many thanks,
Ranjan
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Subject Author Posted

installing AFNI on Fedora 21

maitra March 24, 2015 11:07PM

Re: installing AFNI on Fedora 21

maitra March 25, 2015 12:52AM

Re: installing AFNI on Fedora 21

rick reynolds March 25, 2015 08:47AM

Re: installing AFNI on Fedora 21

maitra March 25, 2015 09:44AM

Re: installing AFNI on Fedora 21

maitra March 25, 2015 10:03AM

Re: installing AFNI on Fedora 21

rick reynolds March 25, 2015 11:23AM

Re: installing AFNI on Fedora 21

maitra March 25, 2015 01:54PM

Re: installing AFNI on Fedora 21

Isaac Schwabacher March 25, 2015 02:26PM

Re: installing AFNI on Fedora 21

maitra March 25, 2015 02:54PM

Re: installing AFNI on Fedora 21 (3dSkullStrip)

maitra March 25, 2015 04:02PM

Re: installing AFNI on Fedora 21 (3dSkullStrip)

maitra March 25, 2015 11:56PM

Re: installing AFNI on Fedora 21 (3dSkullStrip)

rick reynolds March 26, 2015 08:27AM