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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Colm Connolly
August 25, 2016 08:47PM
Thanks for the fix Rick. This now seems to work to a point. afni_proc will now generate a shell script but running it unmasks another error (all 3 of the pre-warped files exist): 

 afni_proc.py -subj_id 107_A -script 107_A.afniRsfcPreprocess.noanaticor.NL.csh -out_dir afniRsfcPreprocessed.noanaticor.NL -blocks despike tshift align tlrc volreg mask blur regress -copy_anat /data/sanDiego/machLearnT1Analysis/data/107_A/107_A.anat+orig.HEAD -dsets /data/sanDiego/machLearnT1Analysis/data/107_A/107_A.resting+orig.HEAD -tlrc_base MNI_caez_N27+tlrc -volreg_align_to first -volreg_tlrc_warp -tlrc_NL_warp -tlrc_NL_warped_dsets /data/sanDiego/machLearnT1Analysis/data/107_A/afniRsfcPreprocessed.NL/107_A.anat_al_keep+tlrc.HEAD /data/sanDiego/machLearnT1Analysis/data/107_A/afniRsfcPreprocessed.NL/anat.un.aff.Xat.1D /data/sanDiego/machLearnT1Analysis/data/107_A/afniRsfcPreprocessed.NL/anat.un.aff.qw_WARP.nii -blur_size 7 -blur_to_fwhm -blur_opts_B2FW '-ACF -rate 0.2 -temper' -mask_apply group -mask_segment_anat yes -regress_censor_first_trs 3 -mask_segment_erode yes -regress_ROI WMe -regress_bandpass 0.01 0.1 -regress_apply_mot_types demean -regress_censor_motion 0.25 -regress_run_clustsim no -regress_est_blur_epits -regress_est_blur_errts
-- tcat: reps is now 256
++ updating polort to 4, from run len 512.0 s
-- importing NL-warp datasets
-- volreg: using base dset vr_base+orig
++ volreg: applying volreg/tlrc xforms to isotropic 3 mm tlrc voxels
-- applying anat warps to 1 dataset(s): 107_A.anat
-- masking: group anat = 'MNI_caez_N27+tlrc', exists = 1
-- will apply motion types: demean
-- have 1 ROIs to regress: WMe

-------------------------------------
** warning have only 1 run to analyze
-------------------------------------

--> script is file: 107_A.afniRsfcPreprocess.noanaticor.NL.csh
    consider the script execution command: 

      tcsh -xef 107_A.afniRsfcPreprocess.noanaticor.NL.csh |& tee output.107_A.afniRsfcPreprocess.noanaticor.NL.csh

+ [[ -f 107_A.afniRsfcPreprocess.noanaticor.NL.csh ]]
+ tcsh -xef 107_A.afniRsfcPreprocess.noanaticor.NL.csh
echo auto-generated by afni_proc.py, Thu Aug 25 17:59:46 2016
auto-generated by afni_proc.py, Thu Aug 25 17:59:46 2016
echo (version 5.02, August 25, 2016)
(version 5.02, August 25, 2016)
echo execution started: `date`
date
execution started: Thu Aug 25 17:59:46 PDT 2016
afni -ver
Precompiled binary linux_openmp_64: Aug 25 2016 (Version AFNI_16.2.13)
afni_history -check_date 1 Dec 2015
-- is current: afni_history as new as: 01 Dec 2015
               most recent entry is:   25 Aug 2016
if ( 0 ) then
if ( 0 > 0 ) then
set subj = 107_A
endif
set output_dir = afniRsfcPreprocessed.noanaticor.NL
if ( -d afniRsfcPreprocessed.noanaticor.NL ) then
set runs = ( `count -digits 2 1 1` )
count -digits 2 1 1
mkdir afniRsfcPreprocessed.noanaticor.NL
mkdir afniRsfcPreprocessed.noanaticor.NL/stimuli
3dcopy 107_A.anat+orig afniRsfcPreprocessed.noanaticor.NL/107_A.anat
++ 3dcopy: AFNI version=AFNI_16.2.13 (Aug 25 2016) [64-bit]
3dcopy afniRsfcPreprocessed.NL/107_A.anat_al_keep+tlrc afniRsfcPreprocessed.noanaticor.NL/107_A.anat_al_keep
++ 3dcopy: AFNI version=AFNI_16.2.13 (Aug 25 2016) [64-bit]
3dcopy afniRsfcPreprocessed.NL/anat.un.aff.Xat.1D afniRsfcPreprocessed.noanaticor.NL/anat.un.aff.Xat.1D
++ 3dcopy: AFNI version=AFNI_16.2.13 (Aug 25 2016) [64-bit]
3dcopy afniRsfcPreprocessed.NL/anat.un.aff.qw_WARP.nii afniRsfcPreprocessed.noanaticor.NL/anat.un.aff.qw_WARP.nii
++ 3dcopy: AFNI version=AFNI_16.2.13 (Aug 25 2016) [64-bit]
** ERROR (nifti_image_write_hdr_img2): cannot open output file 'afniRsfcPreprocessed.noanaticor.NL/afniRsfcPreprocessed.noanaticor.NL/anat.un.aff.qw_WARP.nii.gz'
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Subject Author Posted

afni_proc.py group mask and -tlrc_NL_warped_dsets

Colm Connolly August 25, 2016 02:42PM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

rick reynolds August 25, 2016 04:01PM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

Colm Connolly August 25, 2016 04:02PM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

Colm Connolly August 25, 2016 08:47PM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

rick reynolds August 25, 2016 09:15PM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

Colm Connolly August 26, 2016 11:45AM

Re: afni_proc.py group mask and -tlrc_NL_warped_dsets

rick reynolds August 26, 2016 02:34PM