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  

|
July 25, 2018 08:17AM
Of course

I try
#!/usr/bin/env tcsh
# created by uber_subject.py: version 1.2 (April 5, 2018)
# creation date: Tue Jul 24 21:58:36 2018

# set subject and group identifiers
set subj  = female
set gname = peking

# set data directories
set top_dir = /mnt/e/SemraHoca/Peking/Gr1/${subj}/1860323/session_1
set anat_dir  = $top_dir/anat_1
set epi_dir   = $top_dir/rest_1

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj                                        \
        -script proc.$subj -scr_overwrite                          \
        -blocks despike tshift align tlrc volreg blur mask regress \
        -copy_anat $anat_dir/mprage_noface.nii.gz                  \
        -dsets $epi_dir/rest.nii.gz                                \
        -tcat_remove_first_trs 5                                   \
        -volreg_align_to MIN_OUTLIER                               \
        -volreg_align_e2a                                          \
        -volreg_tlrc_warp                                          \
        -blur_size 6.0                                             \
        -regress_censor_motion 0.2                                 \
        -regress_bandpass 0.01 0.1                                 \
        -regress_apply_mot_types demean deriv                      \
        -regress_motion_per_run                                    \
        -regress_est_blur_errts

My errors or warnings

43 -*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts
-index_to_run_tr $minindex` )

82-*+ WARNING: dataset is already aligned in time!
83-*+ WARNING: ==>> output dataset is just a copy of input dataset

242-*********** Warning *************
Dataset centers are 42.224525 mm
apart. If registration fails, or if
parts of the original anatomy gets
cropped, try adding option
-init_xform AUTO_CENTER
to your @auto_tlrc command.

++ Processing AFNI dataset __ats_tmp___upad40_dset_ns+orig
308-*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
309-*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
310-*+ WARNING: Consider changing the view of the dataset to TLRC view also

356-*+ WARNING: input 'a' is not used in the expression

My version is

Precompiled binary linux_openmp_64: Jul 6 2018 (Version AFNI_18.2.04)

Subject Author Posted

Does it differs to use nii.gz or AFNI format ?

trabz July 24, 2018 04:38PM

Re: Does it differs to use nii.gz or AFNI format ?

ptaylor July 24, 2018 04:49PM

Re: Does it differs to use nii.gz or AFNI format ?

trabz July 25, 2018 08:17AM

Re: Does it differs to use nii.gz or AFNI format ?

rick reynolds July 25, 2018 09:21AM

Re: Does it differs to use nii.gz or AFNI format ?

trabz July 25, 2018 04:08PM

Re: Does it differs to use nii.gz or AFNI format ?

rick reynolds July 26, 2018 11:30AM

Re: Does it differs to use nii.gz or AFNI format ?

trabz July 30, 2018 11:20AM

Re: Does it differs to use nii.gz or AFNI format ?

rick reynolds July 31, 2018 10:18PM

Re: Does it differs to use nii.gz or AFNI format ?

trabz August 01, 2018 10:12AM

Re: Does it differs to use nii.gz or AFNI format ?

rick reynolds August 06, 2018 10:56AM

Re: Does it differs to use nii.gz or AFNI format ?

trabz August 07, 2018 11:30AM