Hi Yuanchao,

Please find the answers below:

Quoting Zhangyuanchao woshizhangyc@yahoo.cn:

Hi,Marie   In the paper "A surface based approach to quantify local gyrification" on TMI. There is a discussion the relation between lGI and curvature-based method. I noticed the following discussion:  "In the current study, all the GI measurements were computed on cortical surfaces based on images in their native space. Independently of intersubject registration, the absence spatial normalization ensures that the observed differences are due to a real decrease in cortical area (related to diminished frequency and depth of sulci) rather than to an effect of scaling."   Given the above discussion, I wonder  whether I should follow the freesurfer processing pipeline in generating the pial surface? If not, how should I manage to obtain the pial surface? since I noticed that in the freesurfer pipeline there is a step called Talairach Transformation. What is the effect of Talairach Transformation on lGI What is the effect of intersubject registration on lGI?

Sou should definitely use the normal freesurfer processing pipeling, where Talairach transformation and intersubject registration do no affect the measurements made in each subjects. I.e. thickness or lgi are measured in the native space and Talairach transformation are made afterwards to estimate the vertexwise correspondence.

When I use lGI to measure cortical folding, whether I should follow the freesurfer pipeline or not since there is intersubject registration in the pipeline?

With lgi you must do exactly how you would do with thickness measurements and statistical comparisons: the normal pipeline measures thickness, curvature, lgi and all other morphometric characteristics in the native images. Then, to compute the statistical comparisons freesurfer estimates the vertexwise correspondence, which is made through different registration process. But these registration process will definitely not affect you prior morphometric measurements. Is that clear?

By the way, in your paper, the radius is 20 or 25, what is the exact default value of the radius in freesurfer?

Default value is 25, you can change it easily

Thanks a lot!

Best regards,   Yuanchao

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