Hi Marco, It’s pretty strange because from the recon-all.log you sent, the first LGI process went fine (line 14584 and 19329 for the right and left hemispheres, on Dec 15). Then you don’t run anything else on the surfaces and just reprocess the exact same LGI process for the same subject (Dec 18), and you get different values from what you just had, with many values <1, plus it gets stuck.
Could that be related to your change on line 51 in make_outer_surface? When you say misalignment, do you mean in freeview or tkmedit? Because we saw some occurrences of misalignment in freeview, which indeed are related to the surface format and as long as the surfaces align well in tkmedit then you should definitely not change anything in the make_outer_surface code. Keep me posted, Marie On 16 Mar 2016, at 02:51, Marco Bucci <bucci.ma...@gmail.com<mailto:bucci.ma...@gmail.com>> wrote: 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.ma...@gmail.com<mailto:bucci.ma...@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<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto: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: mar...@utu.fi<mailto:mar...@utu.fi> **************************************************** <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
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