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tashrifbillah/manual_warp.sh

Created March 1, 2020 18:30
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  1. tashrifbillah created this gist Mar 1, 2020.
    10 changes: 10 additions & 0 deletions manual_warp.sh
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,10 @@
    antsApplyTransforms -d 3 -i /rds/general/user/fmoro/home/bioaxlive/Controls/DTI/London/COB_I078/harm_trial_4/COB_I078_mask.nii.gz \
    -o /rds/general/user/fmoro/home/bioaxlive/Controls/DTI/London/COB_I078/harm_trial_4/COB_I078_mask_resampledWarped.nii.gz \
    -r /rds/general/user/fmoro/home/template_lau4/template0.nii.gz \
    -t /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*[!Inverse]Warp.nii.gz \
    -t /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*GenericAffine.mat

    # if the above does not work, do
    ls /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*[!Inverse]Warp.nii.gz
    ls /rds/general/user/fmoro/home/template_lau4/COB_I078_FA*GenericAffine.mat
    # and replace the last two lines in the former block with absolute paths obtained from the latter