Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Contrast of three groups
by Jacobs H (NP) 29 May '13

29 May '13

Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0 0 0 0 0 0 0.33 0.33 0.33 (first three zeros for the three groups; three zeros for age-correction; three weights for cognition scores)?? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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error loading volume brainmask.gcut.mgz
by Claudia Dacquino 29 May '13

29 May '13

Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia

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Re: [Freesurfer] head motion values
by Joseph Dien 29 May '13

29 May '13

I have a follow-up question for this thread. I'm currently assessing whether to switch from SPM8 to FSFAST. As part of this process, I did a comparison between the SPM8 and the preproc-sess motion correction outputs but found they were quite different for the example data I looked at. Furthermore, I found that the fmcpr.mcdat output and the mcprextreg output are quite different even though they are both generated by fsfast. The following three charts are for mcprextreg, fmcpr.mcdat, and SPM8 respectively. Finally, I'm including a correlation matrix (I don't see any correspondences). The data are actually two separate sessions with a rest break, resulting in a discontinuity at the midpoint. The SPM realignment was run separately on each and as usual the first volume was the reference volume while FSFAST was run on both sessions as a merged set and I think used the middle volume as its reference volume. This shouldn't have resulted in such a large difference between SPM8 and FSFAST though (Ardekani et al 2001 reported they didn't differ that much in accuracy for SPM99 and AFNI98 versions and my understanding is that FSFAST uses AFNI's routine) and certainly not between the two FSFAST outputs. On the other hand, the magnitude of movement in this example is small so I guess my main concern is the discrepancy between mcprextreg and fmcpr.mcdat. I want to make sure I know what I'm looking at and therefore how to use it properly. I looked up the documentation on AFNI's 3dvolreg (http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html) Would I be correct in thinking that mcprextreg results from the -1Dfile option and fmcpr.mcdat results from the -dfile option? I can take this to the AFNI message board once I'm sure where these files came from. Respectfully, Joe > Either fmcpr.mcdat or fmc.mcdat > > On 09/13/2012 02:07 PM, New Fei Ho wrote: > > Hi Doug, > > > > Can you point out the name of file that I should be looking at? > > > > I assumed they were either the mcextreg and mcprextreg output files, but > > these only have 6 columns. > > > > Thanks, > > New Fei > > > >> Hi New Fei, I did some digging and found the docs for the output (pasted > >> below). Translations (displacement) are in mm, rotations are in degrees > >> doug > >> > >> 1. n : time point > >> 2. roll : rotation about the I-S axis (degrees CCW) > >> 3. pitch : rotation about the R-L axis (degrees CCW) > >> 4. yaw : rotation about the A-P axis (degrees CCW) > >> 5. dS : displacement in the Superior direction (mm) > >> 6. dL : displacement in the Left direction (mm) > >> 7. dP : displacement in the Posterior direction (mm) > >> 8. rmsold : RMS difference between input frame and reference frame > >> 9. rmsnew : RMS difference between output frame and reference frame > >> 10. trans : translation (mm) = sqrt(dS^2 + dL^2 + dP^2) > >> > >> > >> On 09/13/2012 11:21 AM, New Fei Ho wrote: > >>> Hi Doug, > >>> > >>> To explicitly clarify, does this mean > >>> X: L-R > >>> Y: Anterior-Posterior > >>> Z: Inferior-Superior > >>> > >>> And are the values of translation/rotation in millimetres? > >>> > >>> Thanks, > >>> New Fei > >>> > >>> > >>>> If by XYZ you mean column, row, slice, then yes. The values are with > >>>> respect to the middle time point (or whatever you used as the > >>>> template), > >>>> it is not the relative difference. > >>>> doug > >>>> > >>>> On 09/12/2012 05:37 PM, New Fei Ho wrote: > >>>>> Hi, > >>>>> > >>>>> I would like to compare the mean head motion between two groups. > >>>>> > >>>>> Just to clarify the values found in the mcprextreg file: > >>>>> 1. Do the six columns represent translationX, translationY, > >>>>> translationZ > >>>>> and rotationX, rotationY, rotationZ? > >>>>> > >>>>> 2. Are the values found in each time-point (i) absolute, i.e. the > >>>>> absolute > >>>>> difference in displacement between this time-point and the middle > >>>>> time-point, or (ii) relative i.e. difference between consecutive > >>>>> time-points? > >>>>> > >>>>> Thanks, > >>>>> Newfei > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>>>> > >>>>> > >>>> -- > >>>> Douglas N. Greve, Ph.D. > >>>> MGH-NMR Center > >>>> gr...(a)nmr.mgh.harvard.edu > >>>> Phone Number: 617-724-2358 > >>>> Fax: 617-726-7422 > >>>> > >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>>> > >>>> > >>>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...(a)nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > >> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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SUMA and FSFAST
by Joseph Dien 29 May '13

29 May '13

I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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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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Freesurfer May 2013