If you want to map the aparc+aseg into the T2 space, then use mri_label2vol (run with --help) or at least use --interp nearest in the vol2vol command

On 4/14/2020 2:35 PM, Agnieszka Sabisz wrote:

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Dear All, I would like to ask you a question. I'm trying to extract values from T2 maps from few brain areas. In my pipeline I miss something and I have a problem to figure out what I'm doing wrong. In the first step, I register my T2w image to T1 (that has got recon-all) 2nd I orient T2_map by registration transformation that is made by bbregister and target it to aparc+aseg.mgz. (T2_map was created from T2w images.) 3rd mri_segstats with a calculation of T2 values My script looks like that:

bbregister --s HTN_Con_083 --mov /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__TE60.nii.gz --t2 --reg /users/work/asabisz/HTN_dane/T2/HTN_Con_083_reg.dat

mri_vol2vol --mov /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__map.nii.gz --targ /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg.mgz --reg /users/work/asabisz/HTN_dane/T2/HTN_Con_083_reg.dat --inv --interp nearest --o /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg2t2.mgz

mri_segstats --seg  /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg2t2.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --id 192 --id 3 --id 42 --id 4 --id 5 --id 7 --id 8 --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 24 --id 26 --id 46 --id 47 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --id 77 --id 85 --id 251 --id 252 --id 253 --id 254 --id 255 --id 2 --id 41 --i /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__map.nii.gz --sum /users/work/asabisz/HTN_analizy/T2/HTN_Con_083_t2.stats

The problem that I have is: I don't get values from --id 192 (corpus callosum) --id 3 and --id 42 - Cerebral Cortex. What I should add to my script? All the best Agnieszka Sabisz

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