Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

LGI computation problem
by Chong-Yaw Wee 04 Jan '14

04 Jan '14

Hi all, I am trying to compute LGI index using freesurfer. However i got the following error message: *Improper assignment with rectangular empty matrix.Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);* Following is the information of my system: *Linux distribution: Linux bass-comp1.cs.unc.edu <http://bass-comp1.cs.unc.edu> 2.6.32-431.1.2.el6.x86_64 #1 SMP Sun Nov 24 09:37:37 EST 2013 x86_64 x86_64 x86_64 GNU/LinuxSUBJECTS_DIR: /home/user_name/software/freesurfer/subjectsCurrent working directory: /server_name/user_name/data/Surface/Command used: recon-all -s subj_folder -localGI* *Matlab version: R2013b (8.2.0.701) 64-bit (glnxa64)* I suspect this error is caused by the Matlab and i have tried the method described in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html to solve it. Unfortunately, i doesn't work for me. Any suggestions to solve it? Thanks, wee

2 1

freeview error {Disarmed}
by Rujing Zha 04 Jan '14

04 Jan '14

Dear Ruopeng, Thanks for your help, Ruopeng.I learned the groupanalysis by manu ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this command on your tutorial data (buckner data). Would you please tell me where my hardware setup is inappropriate? Thanks. All the best. Rujing Zha 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. 2014-01-03 Rujing Zha

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possible to run freeview using other versions of libjpeg.so.62?
by Salil Soman 03 Jan '14

03 Jan '14

Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is it possible to use this version of libjpeg to run freeview (it currently complaints that it cannot find libjpeg.so.62)? If so, can anyone provide info on what symbolic links or environment variables I need to create to do this? Thank you. Salil

1 0

possible to run freeview using other versions of libjpeg other than libjpeg.so.62?
by Salil Soman 03 Jan '14

03 Jan '14

Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is there a way to get freeview to work with a different version of libjpeg (e.g. by making a symbolic link from libjpeg.so.62 to the libjpeg.so.8.0.2 file)? Thanks, -Sal

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Mac Download
by Shazia Dharssi 03 Jan '14

03 Jan '14

Hi FreeSurfer, I was wondering which installation I should use if I am running iOS 10.9.1 Mavericks? Thanks, Shazia

2 1

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

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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

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Freesurfer January 2014