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