Hi Elisa,

It is recommended to use lGI on a vertex-wise basis, i.e. to use qdec the same way you would for cortical thickness. To get access to pial_lgi as a measure of interest in qdec, you need to add a row with: MEASURE1 = pial_lgi in the .Qdecrc file located in your home directory.

Otherwise, if you use mri_segstats, you get for each subject a text file where the rows correspond to the order detailed in "TableCol", i.e. all values after your structure name are lGI values (Mean, StdDev, Min, Max, Range). Don't pay attention to intensity, as you're not giving a volume file as an input lGI values replace intensity values.

Hope it helps,

Marie

Dear FS users,

can anybody help me in understanding the results of the localGI pipeline?

After calling the

recon-all -s subj -localGI

recon-all -s subj -qcache -measure pial_lgi

mri_segstats --annot subj lh aparc --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats

what I obtain is a text file with 10 columns, i.e.

# TableCol  1 ColHeader Index 

# TableCol  2 ColHeader SegId 

# TableCol  3 ColHeader NVertices 

# TableCol  4 ColHeader Area_mm2

# TableCol  5 ColHeader StructName

# TableCol  6 ColHeader Mean 

# TableCol  7 ColHeader StdDev

# TableCol  8 ColHeader Min

# TableCol  9 ColHeader Max

# TableCol 10 ColHeader Range

and 34 rows (i.e. 34 ROIs).

What I cannot understand is the meaning of the last five columns (intensity mean, stdev, min, max, range). Is this "intensity" measure linked to the gyrification index? If yes, how? And, if no, how can I obtain the actual gyrification index?

Thank you.

Best,

Elisa

--

Elisa Veronese - PhD

Research Unit on Brain Imaging and Neuropsychology (RUBIN)

Inter-University Center for Behavioral Neurosciences (ICBN)

University of Udine and University of Verona, Italy

ICBN Website: http://icbn.uniud.it/tiki-index.php

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.