afni.nimh.nih.gov

Hi, afni expert
I am using align_epi_anat and trying to add a weight dataset to adjust the contribution of the cost function. Basically, I have a skullstripped brainmask and want the alignment only consider the cost function that involves brain voxels. I used something like ''-Allineate_opts -weight brainmask.nii.gz". See the full command below

align_epi_anat.py -dset1 /home/stone-ext2/primatemri/site-princeton/sub-032114/ses-001/anat/sub-032114_ses-001_run-2_T1w.nii.gz -dset2 /home/stone-ext2/primatemri/site-princeton/sub-032114/ses-001/anat/sub-032114_ses-001_run-1_T1w.nii.gz -master_dset1 /home/stone-ext2/primatemri/site-princeton/sub-032114/ses-001/anat/sub-032114_ses-001_run-1_T1w.nii.gz -suffix _al.nii.gz -dset1to2 -output_dir /home/stone-ext2/primatemri/site-princeton/sub-032114/anatpp -giant_move -dset1_strip None -dset2_strip None -overwrite -rigid_body -Allineate_opts -weight /home/stone-ext2/primatemri/site-princeton/sub-032114/anatpp/sub-032114_ses-001_run-1_T1w_ssmask.nii.gz

However, it seems that align_epi_anat will automatically generate a brainmask and thus the -weight option will be double set. See the last part of the command output. Can I ask how to pass '-weight' to internal 3dAllineate function??

Thanks.


++ 3dbucket: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit] [0/1842]
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_sub-032114_ses-001_run-1_T1w_ts+orig
#++ Applying threshold of 1158.000000 on /home/stone-ext2/primatemri/site-princeton/sub-032114/anatpp/__tt_sub-032114_ses-001_run-1_T1w_ts+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_sub-032114_ses-001_run-1_T1w_ts_wt -a ./__tt_sub-032114_ses-001_run-1_T1w_ts+orig -expr 'min(1,(a/1158.000000))'
++ 3dcalc: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_sub-032114_ses-001_run-1_T1w_ts_wt+orig.BRIK
#++ Aligning dset1 data to dset2 data
#Script is running (command trimmed):
3dAllineate -lpa -wtprefix ./__tt_sub-032114_ses-001_run-2_T1w_al.nii.gz_wtal -weight ./__tt_sub-032114_ses-001_run-1_T1w_ts_wt+orig -source ./__tt_sub-032114_ses-001_run-2_T1w+orig -prefix ./sub-032114_ses-001_run-2_T1w_al.nii.gz -base ./__tt_sub-032114_ses-001_run-1_T1w_ts+orig -cmass -1Dmatrix_save ./sub-032114_ses-001_run-2_T1w_al.nii.gz_mat.aff12.1D -master /home/stone-ext2/primatemri/site-princeton/sub-032114/ses-001/anat/sub-032114_ses-001_run-1_T1w.nii.gz -weight ./sub-032114_ses-001_run-1_T1w_ssmask.nii.gz -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
++ Authored by: Zhark the Registrator
** FATAL ERROR: Can't have multiple -weight options
** Program compile date = Sep 27 2018
** 3dAllineate failure
** ERROR - script failed