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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

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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 02:42PM
Hi,

I'm trying to rerun some RSFC analysis and in doing so also trying to avoid rerunning nonlinear warping given how long it takes.

I'm running the following command from linux_openmp_64: Aug 19 2016 (Version AFNI_16.2.11) 

 afni_proc.py -subj_id 106_A -script                                                                       \
      106_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/106_A/106_A.anat.zp+orig.HEAD                                 \
      -dsets                                                                                                \
      /data/sanDiego/machLearnT1Analysis/data/106_A/106_A.resting.zp+orig.HEAD                              \
      -tlrc_base MNI_caez_N27+tlrc -volreg_align_to first -volreg_tlrc_warp                                 \
      -align_opts_aea -cost lpc -tlrc_NL_warp -tlrc_NL_warped_dsets                                         \
      /data/sanDiego/machLearnT1Analysis/data/106_A/afniRsfcPreprocessed.NL/106_A.anat.zp_al_keep+tlrc.HEAD \
      /data/sanDiego/machLearnT1Analysis/data/106_A/afniRsfcPreprocessed.NL/anat.un.aff.Xat.1D              \
      /data/sanDiego/machLearnT1Analysis/data/106_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

but am getting the following error 

-- 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): 106_A.anat.zp
** ERROR: cannot apply group mask
** script creation failure for block 'mask'
-- will apply motion types: demean
** regress_ROI: missing ROI dset for 'WMe'
** script creation failure for block 'regress'

Is it not possible to supply previously computed nonlinear warps and apply a group mask?

Thanks,

Colm.



Edited 1 time(s). Last edit at 08/25/2016 02:44PM by Colm Connolly.
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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