Sorry, I forgot to mention that I went back to the original line 51 of the Marie Schaer code in "make_outer_surface". No "fix" anymore.
Marco
2016-03-16 11:51 GMT+02:00 Marco Bucci bucci.marco@gmail.com:
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
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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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