Dear Jesper,
Thank you so much for your time. The exact command line I am using is as
follows:
fnirt --in=IBSR_09_ana_mni.nii --ref=IBSR_03_ana_mni.nii --iout=IBSR09-to-
03_ana_mni_nlr_test7.nii.gz --cout=warp_coef_IBSR09-to-03_test7 --
refmask=MNI152lin_T1_1mm_subbr_mask.nii.gz --
inmask=MNI152lin_T1_1mm_subbr_mask.nii.gz
--aff=IBSR09-to-03_tmp_stage1.mat --config=T1_2_MNI152_2mm.cnf
applywarp -i IBSR_09_seg_subbr_mni.nii.gz -r IBSR_03_seg_mni.nii.gz -w
warp_coef_IBSR09-to-03_test7.nii.gz -o IBSR09-to-
03_seg_subbr_mni_nlr_test7.nii.gz
3dOverlap IBSR_03_seg_subbr_mni.nii.gz IBSR_03_seg_subbr_mni.nii.gz
# Result: 132,771 , this is the original subbr volume
3dOverlap IBSR09-to-03_seg_subbr_mni_nlr_test7.nii.gz IBSR09-to-
03_seg_subbr_mni_nlr_test7.nii.gz
# Result: 167020, this is what we expect to be subbr of IBSR_03
I uploaded all the files of this command with the reference number:945950.
Thanks for your help,
Siamak Yousefi
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