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April 15, 2018 10:42AM
Hi There,

I have created a mask in marsbar. I used AFNI's 3drotate to shift the ROI by 2mm, in a loop that spans the entire superior temporal gyrus, in 2mm increments. It does not matter if I use a loop or not. Entering a single command does the same artifact. Here is code:

for subj in `seq 0 -2 -78`; do
3drotate -prefix /Users/bws35/Brainstuff/MaxLab/Max_fMRI_Preproccesing/STG_extraction_scripts/2mm_slices_STG_union_pole_minus_Herchl_masked_grey_matter/STG_${subj}.nii -bshift 0 ${subj} 0 /Users/bws35/Brainstuff/MaxLab/Max_fMRI_Preproccesing/STG_extraction_scripts/Box_24_22_in_Y_direction_for_STG.nii;
done

When I look at the new ROI in XJVIEW, it has a bunch of red line artifacts in it. If I use SPM display, FSL eyes, or MRICRON - those lines DO NOT show up.

Why would this be, and is this a problem? If I recreate the original with 3drotate, even though in XJVIEW it show the red lines, if I use MARSBAR to extract out beta values, they are identical.

Attached is the original ROI created in marsbar, and one of the results. It has been masked by the STG, but you can see the red lines.

I kindly thank you for your time,
Benson Stevens


Subject Author Posted

3Drotate Attachments

Benson April 15, 2018 10:42AM



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