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  

|
January 14, 2015 08:28AM
Hi-

I have a question. I have data in RPI format, and so was going to use an RPI-resampled standard TT_N27 data set as a Talairach base in afni_proc.

I resampled the dataset:
$ 3dresample -orient RPI -prefix TT_N27_RPI -inset TT_N27+tlrc.HEAD

I have the dataset in directory: ~/REF_TEMPLATES/ .

And my afni_proc command is based on one of the examples:
afni_proc.py -subj_id subj123_D                                \
                  -dsets 2*_EPI.nii.gz  \
                  -copy_anat THR_ANAT.nii.gz \
                  -blocks despike tshift align tlrc volreg blur mask regress \
                  -tcat_remove_first_trs 3                                   \
                  -volreg_align_e2a                                          \
                  -volreg_tlrc_warp                       \
                  -tlrc_base TT_N27_RPI+tlrc \
                  -align_opts_aea -giant_move \
                  -mask_segment_anat yes                                     \
                  -regress_censor_motion 0.2                                 \
                  -regress_censor_outliers 0.1                               \
                  -regress_bandpass 0.01 0.1                                 \
                  -regress_apply_mot_types demean deriv                      \
                  -regress_ROI WMe CSFe                                      \
                  -regress_run_clustsim no                                   \
                  -regress_est_blur_errts

However, when I run the above command, I get the following error:
** failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

In my ~/.afnirc file, I have the following set to point to the said directory:
AFNI_TTATLAS_DATASET = ~/REF_TEMPLATES/
AFNI_GLOBAL_SESSION = ~/REF_TEMPLATES/
AFNI_SUPP_ATLAS_DIR = ~/REF_TEMPLATES/
(with and without final '/')

I have also tried setting the base using absolution paths, as well:
-tlrc_base ~/REF_TEMPLATES/TT_N27_RPI+tlrc \
-tlrc_base /home/paul/REF_TEMPLATES/TT_N27_RPI+tlrc \
with no success.

What am I doing wrong for using this (or any other) data set as a tlrc_base, for the final errts results to end up?

Thanks,
pt
Subject Author Posted

afni_proc.py: failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

ptaylor January 14, 2015 08:28AM

Re: afni_proc.py: failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

rick reynolds January 14, 2015 08:49AM

Re: afni_proc.py: failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

ptaylor January 14, 2015 08:58AM

Re: afni_proc.py: failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

rick reynolds January 14, 2015 09:31AM

Re: afni_proc.py: failed to find tlrc_base 'TT_N27_RPI+tlrc' for group mask

ptaylor January 14, 2015 09:48AM