Hi ,
I am running through the FIRST processing stream , and its first is to execute the command "run_first_all" on T1 images which is not extracted brain . But I saw such a description --After converting all raw data files to .nii.gz, I used fslreorient2std. Following that, I used BET to extract the brain from the skull, and then the FLIRT linear registration in the GUI. These are T1 structural images (2X2X2) and I used an Affine (12 parameter model) with the reference image being MNI152_T1_2mm_brain.
After this, I then used the following:
run_first_all -i con001_brain -b -s L_Hipp,L_Amyg,R_Hipp,R_Amyg \ -o con001 -a con001_brain_to_std_sub.mat ".
Questions: What stages does the script "run_first_all" include definitely when processing T1 images ? Include BET ? Is there anything I should do before it ,such as BET ?
Thank you in advance .
Xin-Fa Shi .
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