and to further this, i added a section on the wiki page on how to use qdec to perform a surface-based lgi analysis. basically, you just do this:
To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage':
recon-all -s my_subject_id -qcache -measure pial_lgi
Do this for each of the subjects in your group.
Then to include 'pial_lgi' as a measure in the 'measures' menu selector in the QDEC Design tab, create a file named .Qdecrc in your $SUBJECTS_DIR/qdec directory containing this text:
MEASURE1 = pial_lgi
This will allow a surface-based group GLM analysis of the lgi measure. You would select 'pial_lgi' in the measures menu (where you will normally find 'thickness' as the default).
N.
On Tue, 2011-07-05 at 22:56 +0200, Marie Schaer wrote:
Hi Ritobrato,
Nick already answered your query. Just a small add: the gold standard to use local gyrification index is to compute vertex-wise analyses rather than parcel-wise comparisons. Indeed, lGI at each point already quantifies the gyrification in the surrounding region. As a result, the average lGI in a given cortical region will also reflect to some (minimal) extent the gyrification in the neighboring gyral regions.
Hope it helps,
Marie
On Jul 5, 2011, at 10:47 PM, Nick Schmansky wrote:
this command can be used:
mri_segstats --annot my_subject_id lh aparc \ --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats
i've updated the lGI wiki page to include this as well.
n.
On Tue, 2011-07-05 at 14:15 -0400, Ritobrato Datta wrote:
Hi All,
I have run
recon-all -s <subj> -localGI
Now I want to get the gyrification Index of a particular label. Is there a way to do that ?
Please let me know
Thanks
Ri
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