Hi Kie Woo,

The other thing that you might want to check is that the pial-outer-smoothed surface and the pial surface match, in case the transformation from the CIVET format induced any strange translation in space and they don't line up. Just open them both on a volume using tkmedit or freeview.

Best,

Marie

On Oct 1, 2015, at 8:54 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Kie Woo

can you run mris_euler_number on those surfaces to see if they are topologically correct?

cheers Bruce

On Thu, 1 Oct 2015, Nam, Kie Woo wrote:

...

Dear experts,

I’m trying to calculate local gyrifcation index using CIVET’s surface file (‘.obj’).

First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created a ‘.pial’ file - below are the commands that worked for ‘CIVET --> FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface -i_fs lh.pial -o_mni lh.pial”

Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the following message.

---

lGI for vertex number 5501 of the outer mesh is 4.1122 lGI for vertex number 5601 of the outer mesh is 0.86156 lGI for vertex number 5701 of the outer mesh is 3.8343 ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high (lGI=62.3205)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.

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The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, but it’s not an option for me because I have no other FreeSurfer compatible files except “.pial”. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html

So, could there be any solution for this?

Best wishes,

Kie Woo

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