Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

Registration & segmentation with FSL - obtaining correlation matrix..
by Sudhin A. Shah 25 Feb '13

25 Feb '13

Hello, This worked perfectly 2 years ago :), but now I am having some trouble. I run reg-feat2anat & aseg2feat with no problem. I now need a correlation matrix of every ROI (created by freesurfer) against every other ROI. For this I used @ROI_Corr_Mat (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) Again - this worked fine in the past. Now I get an error (working with AFNI to see if it can be fixed). Question: Is there any alternative to getting this correlation matrix? i.e every ROI against every other ROI? Thanks, S

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question about MRF
by Zhennan Yan 16 Feb '13

16 Feb '13

Dear freesurfer experts, I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). How can I do this using Freesurfer? (2) If I have several subjects with labels, how can I train the anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my own program? Many thanks! Best, Zhennan -- Zhennan Yan Department of Computer Science Rutgers University

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Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all
by Douglas Greve 15 Feb '13

15 Feb '13

Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: > Hi Doug, thanks for replying, here is the file attached. In case the > attachment doesn't go through please let me know if I should send it > to a different address. > Tudor > > On 18 December 2012 17:34, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Can you send the recon-all.log file (located in the > subject/scripts folder). > doug > > > On 12/18/2012 11:41 AM, Tudor Popescu wrote: > > Hello, > > > > First of all, apologies for asking for help three times today! > THings > > will hopefully become clearer once I get used to FS a bit; I > really do > > appreciate the amazing support provided by the team behind > FreeSurfer! > > > > I ran the following command on one of my structurals: > > > > /recon-all -subject M01 -i M01.nii.gz -all/ > > > > After a few minutes, recon-all ended with the following message: > > > > /Assertion failed at line 827 in file templates/CachedArray.cc/ > > /nu_estimate_np_and_em: crashed while running volume_stats > > (termination status=256)/ > > /nu_correct: crashed while running nu_estimate_np_and_em > (termination > > status=256)/ > > /ERROR: nu_correct/ > > /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > 01:57:59 > > UTC 2009 i686 GNU/Linux/ > > > > I apologise for reporting an error that's already been reported > in the > > past, but unfortunately the solutions suggested in those past > threads > > did not work in my case. To address a few of them: > > > > * my PATH (listed below) does not seem to include two MNI > installations > > > //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ > > * the version of FreeSurfer that I installed is the latest disk > > image available on the website > > (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did > > not see any dev version that would presumably include any > missing > > libraries presumably implied by the above error > > * I tried updating the Xubuntu inside my VirtualBox, however it > > reports an insufficient space problem that from I can see > does not > > have a trivial fix > > > > Advance thanks for any help! > > Tudor > > > > > > _______________________________________________ > > 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: 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. > >

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issue about LME Matlab tools
by ting xu 13 Feb '13

13 Feb '13

Dear all, A few questions come to me when I used LME Matlab toolbox. Then Jorge kindly answered my questions and he also asked me to post our discussion to Freesurfer list so everyone knows what's going on here :) Cheers, Ting ------------------------------------------------------------------- *Subject: *Re: Re: issue about LME Matlab tools *Sent: *Tue, Dec 11, 2012 21:41:26 Hi Ting Please could you post this question to the Freesurfer list, so other people can benefit from this discussion? I'll answer you ASAP. Best -Jorge ------------------------------------------------------ *Subject: *Re: Re: issue about LME Matlab tools *Sent: *Wed, Dec 12, 2012 6:44:36 AM Hi Jorge, Thank you for your explanation in more details. I followed your suggestion, set the convergence epsilon to 10^-5. It truly improved. I am now running the whole brain data, estimations in several voxels were not converge after 50 iterations. Given that iterations takes more computational time, how many iterations do you recommend and what do you usually do if it still not converge? Thank you again:) Warmly regards, Ting ------------------------------------------------------ *Subject:* Re: issue about LME Matlab tools *Sent: *Wed, Dec 12, 2012 00:50:35 Hi Ting You needed more iterations to make the algorithm stop closer to the optimal values. Try: statsFS= lme_fit_FS(X,[1 2],Y,ni,10^-5); or the EM algorithm statsEM = lme_fit_EM(X,[1 2],Y,ni,10^-10); Neither of these algorithms can be guaranty to converge but I have found the FS algorithm to be the most robust and fast. For the mass-univariate setting we limited the number of iterations for the FS algorithm to only 20 due to computational time. Note that for only two repeated measures (as in your data) compound symmetry (a model with a single random effect for the intercept term) likely holds for the covariance matrix among the repeated measures. Although a likelihood ratio test here comparing the model with one random effects against the model with two random effects is barely significant it will not likely survive a multiple comparisons correction. You can not impose structure on D in our toolbox nor it is recommended for general longitudinal data. Let me know any doubt you might have. Best -Jorge ------------------------------------------------------ *Subject: *issue about LME Matlab tools *Sent: *Tue, Dec 11, 2012 14:47:14 Dear Dr. Sabuncu Your recent work "Statistical Analysis of Longitudinal Neuroimage Date with Linear Mixed Effects Models" provided us a great matlab toolbox to apply Mixed Model, especially for imaging data. Now, I am investigating the intraclass correlation based on this toolbox. Sometime I found the function "lme_fit_FS" could not get the accurate estimations. I think the problem may be relevant to the initial value from OLS method, in the case that the within-subject variability estimated from "lme_fit_init" is very close to zero. I attached an example. Y is test-retest imaging data for one voxel, X is design matrix including intercept, head_motion, age, gender. I set random effect for intercept and head_motion. I also attached result from SAS and the model is ok. stats = lme_fit_FS(X,[1,2],Y,ni); Here I'm wondering is there any way to fixed this in matlab? PS, though you have mentioned that no imposed structure on D (covariance matrix of random effect), I am curious if it is possible to define the structure of D in this toolbox. Thanks for your kind attention and look forward to your reply soon. Regards, Ting

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Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
by Narly Golestani 12 Feb '13

12 Feb '13

Post-Doctoral applications are invited 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. 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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bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
by Knut J Bjuland 03 Feb '13

03 Feb '13

When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J

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Inaccurate transformation
by Shani Ben Amitay 03 Feb '13

03 Feb '13

Dear freesurfers I used bbregister to coregister diffusion images with anatomical. I would like to apply the bbregistration transformation to the white and pial surfaces What I've done is: I calculated new transformation matrix using fs_read_dat.m and then apply it to the surfaces with mri_surf2surf. When overlaying the new surface on the diffusion data- it seems that the transformation is inaccurate.(screenshot is attached) Any idea why?. Thanks, Shani

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Reenviar: xhemi registration problem
by Gabriel Gonzalez Escamilla 01 Feb '13

01 Feb '13

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about ROI to SPSS
by xiangbo_2010 01 Feb '13

01 Feb '13

Dear experts I has obtained two ROIs (corrected FDR) difference between AA and GG regressing out the effect of age and gender using the QDEC with attachment, following extract the average surface area of two ROIs to analysis using SPSS, in which I used the Univariate Analysis of Variance to find the difference between AA and GG, gender and age as covariates, but find that there no significant in these ROIs, I want to know why there were significant difference in QDEC, but no significant difference in SPSS? I hope that have experts to help me, thanks! Bo Xiang

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R: Re: R: Re: R: Re: bvecs tracula
by stdp82＠virgilio.it 31 Jan '13

31 Jan '13

Yes Anastasia. To check it, I'm attaching the last bvals,bvecs files (original) and bvals.norot (in my dmri).Thank you very much for your kindness. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 1-feb-2013 0.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: bvecs tracula Hi Stefano - I'm sorry that you're frustrated. Do you mean that you arranged the bvecs as 3 columns (not 3 rows) and are still getting the same error? a.y On Fri, 1 Feb 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I'm frustrated because I'm checking to resolve this problem anywhere but the error is the same. Can it depend from interaction > between fs and new iMAC version (Mountain Lion)? > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 31-gen-2013 22.53 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: bvecs tracula > > > Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula > tutorial for the correct format: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > a.y > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > I attach the bvecs that I'm using. The second is produced in the dmri. > > You are noting that the first is in 3 rows, the second contains only 3 row with a 0 > > > > This is the last error > > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 > > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 > > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff > > #------------------------------------- > > #@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CET > > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref > > /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo > > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat > > #------------------------------------- > > #@# Masks Gio 31 Gen 2013 22:41:55 CET > > #------------------------------------- > > #@# Tensor fit Gio 31 Gen 2013 22:41:55 CET > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > Error: bvecs and bvals don't have the same number of entries > > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; > root:xnu-2050.20.9~1/RELEASE_X86_64 > > x86_64 > > > > trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET > > > > Thanks, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 31-gen-2013 21.43 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] bvecs tracula > > > > > > Hi Stefano - Are the original bvecs (that you specify in your > > configuration file) arranged in 3 rows or 3 columns? > > > > a.y > > > > On Thu, 31 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list, > > > I'm running trac-all -prep -c > > > > > > but I have this error > > > > > > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit > > > Error: bvecs and bvals don't have the same number of entries > > > > > > I'm noting that my original bvecs are > > > > > > 0 -0.460 -0.539 0.490 -0.071 0.226 0.463 0.483 -0.643 0.468 -0.730 -0.707 -0.318 0.175 0.488 0.460 > > > 0 -0.395 -0.588 -0.706 -0.605 -0.607 -0.236 -0.180 -0.464 -0.562 -0.337 -0.699 -0.786 -0.786 -0.712 -0.301 > > > 0 -0.795 0.419 -0.057 -0.793 -0.725 -0.708 -0.695 -0.609 0.333 0.413 -0.108 0.368 0.392 -0.004 0.476 > > > > > > and in dmri > > > > > > 0 > > > 0 > > > 0 > > > > > > bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format? > > > > > > Thank you very much, I really appreciate your patience. > > > > > > Stefano > > > > > > > > >_______________________________________________ > > 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. > > > > > > > >_______________________________________________ > 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. > > > >_______________________________________________ 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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Freesurfer January 2013