Freesurfer

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30096 discussions

mri_anatomical_stats on custom 'thickness' file
by Martijn Steenwijk 29 May '13

29 May '13

Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 'thickness' input? Or does mri_anatomical_stats something more complex than just averaging the values inside each region? Best, Martijn

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Representation of average curvature on subject's curvature
by Sophie Maingault 29 May '13

29 May '13

Hi FreeSufer Experts, I would like to do a figure like this one published in High-Resolution Intersubject Averaging and a Coordinate System for the cortical Surface (1999, Fischl et al.). I would to superimpose the isocontour of average curvature (for example fsaverage) on a subject's curvature before and after registration. How can I do this with tksurfer ? Thanks a lot for your help ! Sophie

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LME toolbox - univariate
by Yolanda Vives 29 May '13

29 May '13

Dear FreeSurfer experts, I am trying to use the LME toolbox to analyse the hippocampal change over time in a group and also among 2 groups (2 scans per subject). When I estimate the parameters with lme_fit_FS I become a warning saying that the matrix is singular and my results are NaN. I guess that my design matrix X is not correct, can you please help me? I have followed the example from the wiki. My model for the two groups study is the following: Yij = ß1 + ß2*tij +ß3*Group1 + ß4*Group1 *tij + ß5*Group2 + ß6*Group2 *tij+ ß 7*Genderi + ß8*Agei + ß9*ICVi + b1i + b2i*tij + eij 1) intercept (all ones) 2) time (tij) . Here I have 0s for the first scan of each subject and a number in years for the second scans. Is it correct? 3) one for Group1 and zero otherwise 4) colum 3) .* time 5) one for Group2 and zero otherwise 6) colum 5) .* time 7) Gender 8) Age of the subject at each scan moment. 9) ICV (converted to liters). Thank you in advance, Yolanda

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Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
by Narly Golestani 29 May '13

29 May '13

Applications are invited for a funded Post-Doctoral position in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. The work will be supervised by Narly Golestani and Dimitri Van De Ville. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch.

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Subcortical Structures not included in GM surfaces
by Jonathan Holt 28 May '13

28 May '13

Is this normal, attached slide shows a rather common occurrence for me. Half of the amygdala (blue) is included in pial surface, while the other is not. How should I go about fixing, the local WM is perfectly fine so I'm not sure where to start.

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recon-all error: v5.0.0 - dataset 1
by Sudhin A. Shah 28 May '13

28 May '13

BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013

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hipposubfields and data
by Joshua Lee 28 May '13

28 May '13

I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm? Josh

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recon-all error: v5.0.0 - dataset 2
by Sudhin A. Shah 28 May '13

28 May '13

=============== *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 ==============

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recon-all error: v5.0.0 - dataset 3
by Sudhin A. Shah 28 May '13

28 May '13

CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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Re: [Freesurfer] mri_anatomical_stats segmentation fault
by Douglas N Greve 28 May '13

28 May '13

Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have that many veritices, then that could cause the problem. doug On 05/28/2013 10:33 AM, Rob Tennyson wrote: > Hi Doug, > > Attached are the three labels I'm having an issue with (each with a > different subject). These are built from areas that we found > functional differences between a healthy control group and a MDD > group. I was going to take a look at the anatomical stats to see if > there are thickness or volume differences as well. > > I am also going to review the white surface soon as Bruce suggested. > > > On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Rob, can you send me your label? > > doug > > On 05/27/2013 01:00 PM, Rob Tennyson wrote: > > Hi All, > > > > I'm running "mris_anatomical_stats" with a few manually defined > > labels. For a few of my subjects, I am getting the error: > > "Segmentation fault" on one of the labels. However, the other > manually > > defined labels process without any errors on these same subjects. > > > > For example, I am running "mri_anatomical_stats" on subject 33_bay6 > > with a manually defined ERC label, a manually defined PHC label, > and a > > manually defined medial frontal gyrus label. The only label that > runs > > an error for this subject is the PHC label. This PHC label runs > > without any errors on the rest of my subjects. > > > > Here is what is displayed when running a label that fails: > > > > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b > > 33_bay6 lh > > limiting computations to label lh.PHC_1.label. > > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... > > reading input surface > > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > > reading input pial surface > > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... > > reading input white surface > > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... > > Segmentation fault" > > > > Does anyone know what may be causing the Segmentation fault and what > > steps I should take to fix it? > > > > Thank you for your help! > > Rob > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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