MC subjects for Timmy

[finnlennartsson]

Go through all scans in /sourcedata for Quality Control (QC) of motion-artifacts.

[finnlennartsson]

Example for generating a tsv-file (here tagged with _LU) and putting eligible scans in it.

# Generate tsv-file
echo -e "Subject_ID\tfile\tQC_MC_fail_or_pass\tQC_signature\tComment" > $HOME/MC_QC_LU.tsv

# Go through all anatomy scans and put in the tsv-file
for subj in sub-10*; do
echo $subj; files=`cat $subj/*.tsv | grep anat/${subj} | awk '{print $1}'`; 
for file in $files; do 
echo $file; 
echo -e "$subj\t$file\t\t\t" >> $HOME/MC_QC_LU.tsv; 
done; 
done

[finnlennartsson]

# Go to /sourcedata folder
cd /home/hickmat/Research/Projects/BoF_309_LIM_NEW/sourcedata

# Now use the file MC_QC_LU.tsv-file (in $HOME) to visualise all T2w images (MCRIB and some SPC)
for file in `cat $HOME/MC_QC_LU.tsv | grep T2w | sed 's/\tanat/\/anat/g'`; do 
mrview $file -mode 2; 
done

[finnlennartsson]

How to judge QC:

• QC_MC_fail_or_pass = 1 = PASS No artifacts. Draw-EM can be used without probs.
• QC_MC_fail_or_pass = 0.5 = BORDERLINE Some artifacts. Should effect result from Draw-EM, but it is unclear to what extent.
• QC_MC_fail_or_pass = 0 = FAIL Artifacts. Cannot be used with Draw-EM as it is now.

Example of how to judge QC

• QC_MC_fail_or_pass = 1 Example 1 Comment: No motion, but we have discrete sequence/recon-related inter-slice-stack zig-zag bumps. Example 2 Comment: No motion, but we have discrete sequence/recon-related inter-slice-stack zig-zag bumps.

• QC_MC_fail_or_pass = 1 or 0.5 Example Comment: No motion, but we have a bit more pronounced (compared to above) but still only subtle sequence/recon-related inter-slice-stack zig-zag bumps.

• QC_MC_fail_or_pass = 0.5 Example 1 Comment: Head shaking motion (side-to-side) giving motion artifacts and zig-zag pattern along cortex. Mainly in the frontal lobes and best visible in the COR plane

• QC_MC_fail_or_pass = 0 Comment: moderate motion artifacts