Dear all,

I forward again my original post.

I also attach the recon-all.log of one of the several faulty cases.

I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0)

 in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a

and I have fixed the SearchProjectionOnPial.m.

I also had to fix line 51 of make_outer_surface.m

"v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation"

with

"v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) vol.vox2ras1(3,4)-v(:,2)];"

in order to use the image coordinate to fix surface orientation and alignment.

If I would use the original line 51, the surface produced by recon -lgi results

misaligned with the reference pial and image.

My problems remains the aberrantly high lgI value in most of my subject images.

Can you help me?

Yours,

Marco Bucci

---------- Forwarded message ----------
From: Marco Bucci <bucci.marco@gmail.com>
Date: 2015-12-22 23:49 GMT+02:00
Subject: Re: [Freesurfer] lGI value is aberrantly high
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>


Dear all,

I have a problem with the LGI module.
At the step when the software computes the LGIs for the vertices,
In one vertex the lGI results aberrantly high and the software exits
with ERRORS.

I tried the solution suggested by Marie Schaer to rereconstruct
The images with "randomness"
Recon-all -autorecon2-wm -randomness -autorecon3

I tried this fix on two of my subjects
With errors. Not all subject resulted
Errors in the computation of the gyrification.

Can you help me?

Marco Bucci
Turku Pet Center

Sent from my iPhone

--

****************************************************
Marco Bucci, PhD in 

Clinical Physiology and Nuclear Medicine

Turku PET Centre
Turku University Central Hospital (TUCH)
PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland
tel. +358 2 3132798
fax. +358 2 2318191
mobile: +358 40 6873976
UTU e-mail: marbuc@utu.fi
****************************************************

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