Freesurfer

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30133 discussions

Tutorial for linear mixed model toolbox
by sabin khadka 03 Jan '14

03 Jan '14

Hi all, I was just wondering if there is a tutorial or example on how to use linear mixed effect model toolbox for longitudinal analysis. I already processed my structural images with longitudinal processing pipeline from freesurfer. I want to do group analysis where I have 4 groups with N~20-30 on each group for time T1 and T2 scans in duration of ~2 years. I am kind of in confusion on how to proceed like making qdec.table.dat and contrast matrix and all. Thanks for help!!!! -- Cheers, Sabin

2 1

Total number of vertices participating in boundary based register
by Jörg Pfannmöller 03 Jan '14

03 Jan '14

Dear FreeSurfer experts, in the publication 'Accurate and robust brain image alignment using boundary-based registration', by Greve and Fischl (2009), in formula 2 a quantity termed N occurs. It is described as:'N is the total number of vertices participating'. Can I find this N in the files created by BBR? I inspected the files and found in register.dof6.dat.sum the following entries: Final costs ---------------- Number of surface hits XXXXX and nhits= XXXXX. Both entries are equal and seem to be the N, which I am interested in. Can you please tell me if this is right. Sincerely yours Joerg

1 0

Difference between -autorecon2 and -autorecon2-cp
by Kaiming Yin 02 Jan '14

02 Jan '14

Hi, A little confusion here, when I add the control points after edits, should I run -autorecon2 or -autorecon2-cp? Another question is about the starting stage of autorecon2-cp, i.e. stage 10+ or stage 12+, which are stated differently on the wikipage and tutorial. Happy New Year! Thanks, Kaiming

1 0

Motion correction for SPACE FLAIR
by Octavian Lie 02 Jan '14

02 Jan '14

Dear All, We recently implemented pial correction using T2 space FLAIR with freesurfer v 5.3, mostly successfully. We use 2-3 MPRAGE (sagittal + axial and/or coronal) volumes as 001.mgz, 002/003.mgz for the motion correction step in recon-all pipeline. The typical times for acquiring space FLAIR in our settings vary from 2.5 to 6 min, depending on the resolution/NSA no. I was wondering how freesurfer deals with motion artifacts in the space FLAIR sequence (especially with longer acquisition times), and if there is a strategy to minimize motion distortion with these (such as getting second runs for averaging, etc). Please advise, Octavian.

2 1

missing libnetcdf.so.6 on ubuntu for TRACULA
by Salil Soman 31 Dec '13

31 Dec '13

Dear Anastasia, I am using the latest tracula code (CentOS 6 64 bit on an ubuntu 13 machine) and FS 5.3 to rerun cases I had processed with the previous version of tracula using the new code and am getting the following errors: *freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory* and also after the bvecs and bvals files are copied to the output directory: *xx: Subscript out of range.* I have set LD_LIBRARY_PATH to include /usr/lib (where libnetcdf.so.7.1.1 is located) and a separate directory where I have made a link from libnetcdf.so.6 to /usr/lib/libnetcdf.so.7.1.1. Any suggestions would be greatly appreciated. Best wishes, Sal

1 0

freeview error
by Rujing Zha 31 Dec '13

31 Dec '13

Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button "configure overlay". Then freeview were suspended. The CPU ran "100%",and memory ran "23%". There was nothing to do but terminated it manually in the command console by "ctrl + c". I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is "NVIDIA GeForce 8600 GT", and CPU is "Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz", and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha

3 4

Obtaining the center of mass coordinates of a label file
by Omar Singleton 31 Dec '13

31 Dec '13

Dear Freesurfer Community, Does anyone know of a way to get the coordinates of the center of mass of a FreeSurfer label? Is there any way of doing this? Thanks! Best, Omar

1 0

citation for smoothing method
by YUMI MAEDA 30 Dec '13

30 Dec '13

Hi, I have a question about citation for smoothing methods. In the following link, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer there are statement " ....This data was smoothed in the volume at 5mm, but when preparing for a group surface-based analysis, we recommend that you smooth on the surface prior to group analysis and not smooth in the volume at all (or less than the voxel size) ...." Is there any reference paper that I can cite when I write a manuscript? thank you very much. YUMI

2 1

mri_mask output problem
by Caspar M. Schwiedrzik 30 Dec '13

30 Dec '13

Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar

2 6

freeview error
by Rujing Zha 30 Dec '13

30 Dec '13

1 0

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