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  

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February 17, 2015 03:14PM
Dear AFNI team members,

I installed AFNI in my home directory: /Users/Sampada/abin and I have a python script for resting state MRI analysis in /Users/Sampada/Desktop/mb_niftifiles_all. However, when I run the following command to run my script in a bash shell using


Last login: Mon Feb 16 12:00:56 on ttys002
rmbp:~ Sampada$ cd /Users/Sampada/Desktop/mb_niftifiles_all/
rmbp:mb_niftifiles_all Sampada$ ./2_funcpreproc_U01-2.sh
---------------------------------------
!!!! PREPROCESSING FUNCTIONAL SCAN !!!!
---------------------------------------
./2_funcpreproc_U01-2.sh: line 45: cd: /Users/Sampada/Desktop/mb_niftifiles_all/mb_resting.nii
Dropping first TRs
./2_funcpreproc_U01-2.sh: line 59: 3dcalc: command not found
Deobliquing 7394
./2_funcpreproc_U01-2.sh: line 63: 3drefit: command not found
Reorienting 7394
./2_funcpreproc_U01-2.sh: line 68: 3dresample: command not found
Motion correcting 7394

Will you please let me know how do I connect the afni to my script to make it work??

Much thanks for your time.

Kind regards,

Sampada
Subject Author Posted

Regarding: Sourcing AFNI to run my resting state python script

Sampada February 17, 2015 03:14PM

Re: Regarding: Sourcing AFNI to run my resting state python script

rick reynolds February 18, 2015 09:14AM

Re: Regarding: Sourcing AFNI to run my resting state python script

Sampada February 18, 2015 12:46PM

Re: Regarding: Sourcing AFNI to run my resting state python script

rick reynolds February 18, 2015 12:50PM