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tashrifbillah/manual_warp.sh

Created March 1, 2020 18:30
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Help @fedemoro with debug
Raw
manual_warp.sh
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
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