I forward again my email, that has not been sent to the mailing list yet.
---------- Forwarded message ---------- From: Marco Bucci bucci.marco@gmail.com Date: 2016-03-22 10:05 GMT+02:00 Subject: Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Dear Marie and Freesurfer Users,
thanks for your support. I could not imagine that freeview was visualizing wrongly the surfaces.
For this reason, my colleague and I have added a small "integrity check" with which we compare the min and max of the vertexes coordinates of pial and pial-outer. If the pial min and max are closer to the center it means that pail is included in the outer surface. We believe this is faster than checking visually with the viewer all the surfaces, slice by slice.
The subject surfaces of which I sent you the recon.log passed the test. But... I ran another case and unfortunately it did not pass the check. I attach the recon log, the screenshot of tkmedit with lh.pial going below the outer surface. Is it important for the lgI calculation purposes?
I also attach the Matlab code for the testing (it is rough, but works) It is possible to check with a stepsize of 1 to be absolutely sure about any intersection, but it takes longer time.
Looking forward to hear from you soon.
Thanks in advance for your help
Yours, Marco (and Harri)
P.S. I went back to the original line 51 of the Marie Schaer code in "make_outer_surface". No "fix" anymore.
2016-03-17 23:19 GMT+02:00 Marie Schaer Marie.Schaer@unige.ch:
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.marco@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.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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