Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

Aseg stats and white surfaces
by Michael Harms 22 Dec '07

22 Dec '07

Hello, In FS v4.0.1 the Aseg Stats stage now occurs toward the end of the recon-all script, and is designed to use the "--surf-wm-vol" flag if both the lh.white and rh.white surfaces exist. Just wanted to point out that if any subsequent edits are made resulting in changes to either lh.white or rh.white (e.g. as a consequence of making edits and then running either -autorecon2-cp, -autorecon2-wm, or -autorecon2-pial), the values for "cerebral-white-matter" volume contained in aseg.stats will no longer reflect the true volume for the current ?h.white surfaces, since Aseg Stats is not automatically rerun as part of those flags. Perhaps "set DoSegStats = 1" should be included as part of any flag that results in new ?h.white surfaces? cheers, Mike H . -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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anatomical stats in stable-pub-v3.0.5
by Paul Greenberg 21 Dec '07

21 Dec '07

Hi All, I've processed a set of 40 subjects with freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 and am now working on a series of morphometric analyses. I am comparing gray matter volumes found in: 1) aparc.stats from recon-all, (same as output of "mris_anatomical_stats" run from the command line) 2) "mris_volume" run from the command line for each hemisphere. I'm seeing slightly different results for the same subject and was wondering why. ** From aparc.stats, I see an initial value of 197405 mm3. This includes a column of data labeled corpus callosum that I assume is not gray matter. Subtracting that, I get 196549 mm3 for a single subject. I'm assuming that the corpus callosum value found in aparc.stats, though small, ought to be removed when calculating total gray volume per hemisphere? ** Running the command line option "mris_volume rh.pial" , followed by "mris_volume rh.white" and subtracting the two values I get 193215 mm3. This is 4190 mm3 smaller than the initial values from aparc.stats for that subject. The question: Are these differences expected? Which value is better to use, and why? Would the general cause of these differences in cortical gray matter volume quantification be consistent for all subjects? Thanks very much, Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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Cerebellar surface?
by Paul Greenberg 21 Dec '07

21 Dec '07

Hi all, Are there any plans for freesurfer to create a cerebellar surface rendering suitable for the display of fMRI results, or is 3D Slicer a good option for creating a 3D cerebellum from the aseg parcellation? Thanks much and happy holidays, Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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jacobian analyses
by Michael Harms 21 Dec '07

21 Dec '07

Hello, I'm going back and running the jacobian analyses (using v4 recon-all) so that I can look at distortion arising from the spherical registration. Couple questions about what is going on "under the hood": 1) When using the -jacobian_white flag, the command executed is: mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white Why the use of ?h.white rather than ?h.sphere as the "original surface"? 2) When using the -jacobian_dist0 flag (which appears to be analogous to the old -jacobian flag in the recon-all from v3) the input surface used is ?h.sphere.reg. If I understand correctly, this means that the resulting ?h.jacobian_dist0 file reflects the ADDITIONAL distortion that ensues when registering the already partially registered ?h.sphere.reg to the average convexity of the target atlas with the distance constraints turned offf. Is that concept of "additional" distortion the correct way to think about the ?h.jacobian_dist0 data? 3) In terms of Eq (5) from Fischl et al 1999 ("High-Resolution Intersubject Averaging..."): J = J_p + A*J_a + D*J_d Are BOTH constants A and D set to zero by the -dist0 flag in mris_register (or is it just D that is set to zero)? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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question about control points
by Matt Colvin 21 Dec '07

21 Dec '07

Freesurfer Folks, I am having trouble with a handful of subjects in which there are portions of white and grey matter not included by the white and pial surfaces. The problems at hand seemed like good candidates for control points, so I added some and have run recon2-cp on these subjects (in FreeSurfer v 4.0.1). I am having limited success fixing the problems, especially in the temporal lobes, and have attached a couple screen caps of one of the more egregious problems. Most of the voxels I believe to be white matter are in the 100-110 range of intensity. If it can be guessed at from these screen shots, is there some principle of using control points that I am not getting right? Also, would editing the wm.mgz file be another possible avenue of fixing the problem? As always, thanks in advance. --Matt Colvin

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ERROR: talairach_afd: Talairach Transform:
by Roberto Roiz Ssantiáñez 21 Dec '07

21 Dec '07

Dear all. I have tried to run recon-all -s subject -autorecon1 with a sequence acquired in a 3T Philips scanner. I have transformed the image into Analise using MRIcro and then run recon-all. I got the following error: talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Fri Dec 21 16:24:50 CET 2007 /usr/local/freesurfer/subjects/roberto/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux roberto-desktop 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT 2007 i686 GNU/Linux recon-all exited with ERRORS at Fri Dec 21 16:24:50 CET 2007 However when I do the same wit ha different sequence acquired in a 1.5 GE scanner everything runs nice. Any idea where the problem could be? Best wishes and Happy Christmas Roberto

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Regarding QDEC Figure
by ppj＠netfilter.com.br 20 Dec '07

20 Dec '07

In the attached figure: The numbers (-28.25, -12.73, -0.57) refer to fsaverage. How can I export the Thickness values of the subjects for this cordinates? The numbers (-28.25, -12.73, -0.57) are in Talairach space? Thanks, PPJ

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Re: [Freesurfer] Regarding QDEC Figure
by Pedro Paulo Oliveira Jr 20 Dec '07

20 Dec '07

I can dig into the code, but do you know how qdec extract the values to that graph? thanks, Pedro Paulo on E61 -- mens. original -- Assunto: Re: [Freesurfer] Regarding QDEC Figure De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Data: 20/12/2007 20:44 Hi Pedro, the mapping from tal to surface isn't well defined as there will be many tal coords that are not on the surface. You could find the closest point on the surface to a given coord, but many coords will have the same closest point cheers, Bruce On Thu, 20 Dec 2007 ppj(a)netfilter.com.br wrote: > In the attached figure: > > The numbers (-28.25, -12.73, -0.57) refer to fsaverage. How can I export > the Thickness values of the subjects for this cordinates? > > The numbers (-28.25, -12.73, -0.57) are in Talairach space? > > Thanks, > > PPJ

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3D reconstruction of supratemporal plane
by Tanji, Kazuyo (NIH/NIMH) [F] 20 Dec '07

20 Dec '07

Hi, I am looking for a way to do 3D reconstruction of the supratemporal plane just as it was done in a Neuroimage paper by Sigalovsky et al., 2006. In other words, I would like to remove frontal and parietal opercula to expose the supratemporal plane in the reconstructed brain. I heard that it is possible with freesurfer. Could someone suggest how I can do this? Thanks, Kazu

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Two questions regarding Matlab
by Pedro Paulo Oliveira Jr 20 Dec '07

20 Dec '07

Sorry for the stupid questions, I promise to put it on the FAQ after the answers: 1) Is it possible to use Octave instead Matlab for curv files? 2) Given a Talairach coordinate how can I get the thickness value in Matlab? Thanks in advance Pedro Paulo Jr

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Freesurfer December 2007