Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

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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Qdec with v3
by Michael Harms 20 Dec '07

20 Dec '07

Hello, We are getting ready to do some surface analyses on data processed under v3.0.4 or v3.0.5. We would like to try using the Qdec utility from FS v4 to analyze this v3 data. Is that a legitimate thing to do? I see that at a minimum, we will need to run recon-all -s <subj> -qcache (under FS v4) to generate necessary files expected by Qdec. The various surfaces for the 'fsaverage' subject differ between v4 and v3. Obviously, running -qcache under v4 will use the v4 'fsaverage' subject. Provided we then also link to the v4 'fsaverage' subject for display purposes, I'm assuming that we'll be in proper correspondence. Is that correct? v3 and v4 also have different .gca and .gcs atlases. But I don't need to worry about that in terms of using Qdec, right? Is there anything else I'm missing that would need to be done, or why Qdec (v4) can't be used on v3 processed data? 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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Fixing a bad talairach
by Caroline Chapman 19 Dec '07

19 Dec '07

Hi Freesurfers, Happy Holidays! I have a subject failing at Intensity Normalization, and upon checking the talairach, I found that it is very bad. When loaded in tkregister2, the talairach is off the screen, and the orientation is off--coronal is matched to saggital). According to the wiki instructions, I will need to correct the transform. Is it possible to fix this bad talairach in tkregister2? If it is helpful, I have the error message from the Intensity Normalization error printed below. Thank you! Caroline mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.484 1.141 -0.183 -61.600; -1.154 0.466 -0.149 -62.214; -0.067 0.226 1.231 276.948; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux node0072 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Tue Dec 11 15:16:05 EST 2007 -- Caroline Chapman Research Assistant/Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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ENC: Re: Optimizing FreeSurfer
by Pedro Paulo Oliveira Jr 19 Dec '07

19 Dec '07

Hello, I have a couple of questions, not so technical. A) In your opinion what would be the best measure for comparing number of neurons among subjects: Average cortical thickness or Volume of White matter. B) Automatic parcelation and atlas based segmentation is a valid approach for patients with severe cortical malformation? Thanks in advance for your help. Best Regards Pedro Paulo Jr.

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fsl + freesurfer
by Gui Xue 19 Dec '07

19 Dec '07

Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis. what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them. It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis. but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space. but then I am not sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects). any help will be greatly appreciated. Gui

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