Hi, Experts,

I previously created a mask with the method below, as a mask is required for the group analysis, e.g,. 3dttest++

3dmask_tool -input Sub*/*BrainMask+tlrc.HEAD \
-prefix mask_overlap.7 \
-frac 0.7

Sub*/*BrainMask+tlrc.HEAD stands for the brainmask from all subjects. All in all, this step generates a mask for the 3dttest++ and/or ANOVA2 analysis. Suppose my output is, Reward_vs_Neutral_ShapeNonfixed+tlrc.BRIK, Reward_vs_Neutral_ShapeNonfixed+tlrc.HEAD

I am not very confident with this step. Is this approach fine? Is this mask great for me to track all activation in grey matter and brain stem?

I got to know that there is another approach to make the mask, but not very clear.

For instance, people use the TT_N27_grey_seg.nii.gz (get it from the TT_N27+tlrc, using the FAST tool, FSL). Could you advise which method below is correct? I was thinking that the 2nd line is correct. Right? I am not clear why some use the 1st line.

3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -expr 'a*step(3-a)'
3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -expr a

Then they use the line below to get the final template,
3dfractionize -template ./Reward_vs_Neutral_ShapeNonfixed+tlrc. -clip 0.2 -preserve -prefix TT_N27_grey_seg_short_F -input TT_N27_grey_seg_short+tlrc.

I am also confused why here the template need be the output from the group analysis (i.e, Reward_vs_Neutral_ShapeNonfixed+tlrc). It looks like a circular argument, as we want to get a mask for the next group analysis (e.g., 3dttest++ and/or ANOVA2). But here the template is from the group analysis output. Something must be wrong. Any good pointers?

Thank you for your time,
J



Edited 1 time(s). Last edit at 12/28/2020 02:01AM by Juan.