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Local Gyrification Index (LGI)

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Vlad Drobinin edited this page Jun 14, 2021 · 1 revision

Local Gyrification Index - LGI

This requires a successful run of the minimal preprocessing pipeline on the participants of interest.

Theoretical

Gyrification index is a metric that quantifies the amount of cortex buried within the sulcal folds as compared with the amount of cortex on the outer visible cortex. A cortex with extensive folding has a large gyrification index, whereas a cortex with limited folding has a small gyrification index. More information is available here.

In essence after the HCP minimal preprocessing pipelines are done you cd into processed T1w directory. (Don't actually do this)

 export SUBJECTS_DIR=`pwd`

Then run the command below, which will work on the participant ID in the T1w folder.

recon-all -s participantID -localGI

This takes just under 2 hours per participant and produces right and left .pial_lgi in the surf folder. To generate statistics on ROIs, run (and again for right hemisphere):

mri_segstats --annot 000_VD_A lh aparc --i $SUBJECTS_DIR/SSID_A/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats

You get LGI values for 34 ROIs of the FreeSurfer Desikan atlas.

Practical

To automate, we use scripts instead

  1. cd into data folder /shared/uher/FORBOW_Brain/neuro_data/Biotic3T and run /bin/ls -d 0??_A to display baseline scans in a line. Copy the participants needed to run. Or just do this manually if only processing one or two.

  2. In order to run multiple subject simultaneously, will use GNU parallel. First type: parallel -j n where n is the number of simultaneous jobs. Memory usage 5-6GB per subject puts us at 3-4 subjects max (can do 12 with new workstations).

  3. Then, drag LGI_0_run_freesurfer.sh from the _scritpts folder to terminal and specify participants that need to be run (space separated). Example of full command: parallel -j 3 /shared/uher/FORBOW_Brain/neuro_data/Biotic3T/_scripts/LGI_0_run_freesurfer.sh ::: 031_A_NP 032_A_NP 035_A 035_A_FLAIR 035_A_NP 036_A 036_A_NP 036_A_FLAIR

  4. Finally to get the stats for the ROIs run the LGI_collate_results2csv.shscript

  • specify participants to run (space separated - usually a good idea to get stats on all)
  • if needed can edit script to specify structures of interest
  • check _results folder for CSV file
  • to run this on all participants, drag the script into the terminal window and follow with: '/bin/ls -d 0??* 1??*'
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