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.ma...@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.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" <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 > **************************************************** > > _______________________________________________ > Freesurfer mailing list > 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. > > -- **************************************************** 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 ****************************************************
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