Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

NIfTI-1 convert
by Kirk, Gregory 23 Jun '06

23 Jun '06

Hi folks, I want to use mri_convert to convert 30 direction diffusion data to NIfTI-1 format. I ran it and it seemed to work good. I just wanted to clarify one thing. The docs seem to say that unless I use --conform it will not interpolate my data to 1mm res, or change it in any way. Is that the correct interpretation ? don't think I should be interpolating my diffusion data before I feed it to FSL. cheerio Greg.

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volumes
by Sasha Wolosin 23 Jun '06

23 Jun '06

Dear All, Is the total white matter volume computed by mris_anatomical_stats the total volume inside the gray/white surface? Or does it exclude subcortical structures? i.e. is total brain volume = total gray matter volume + total white matter volume ? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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mris_fix_topology
by dasoscia＠buffalo.edu 23 Jun '06

23 Jun '06

I think my fix topology sequence froze...I typed "top" in another terminal and this is what came up... ID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 899 surf 25 0 2169m 1.6g 1984 R 99.1 43.1 1042:33 mris_fix_topolo 18609 root 15 0 457m 196m 8616 S 0.7 5.3 23:08.06 X 18768 tinnitus 16 0 7088 2920 856 S 0.3 0.1 18:04.16 gam_server 1453 surf 17 0 6148 1000 752 R 0.3 0.0 0:00.42 top According to this, my mris_fix_topogy has been running for over 17 hours, and I have a brand new, extremely fast computer. Here's what the other terminal says... #@# Fix Topology lh Thu Jun 22 15:08:24 EDT 2006 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/surf/freesurfer/subjects/DOD16-11-1-05/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga DOD16-11-1-05 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.3 2006/04/12 02:03:02 nicks Exp $ before topology correction, eno=-1199 (nv=137208, nf=276936, ne=415343, g=600) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 17 iterations marking ambiguous vertices... 163949 ambiguous faces found in tessellation segmenting defects... 93 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 24 into 0 -merging segment 27 into 0 -merging segment 31 into 0 -merging segment 29 into 7 -merging segment 34 into 7 -merging segment 37 into 7 -merging segment 38 into 7 -merging segment 43 into 7 -merging segment 55 into 7 -merging segment 57 into 7 -merging segment 63 into 7 -merging segment 78 into 7 -merging segment 80 into 7 -merging segment 82 into 7 -merging segment 87 into 7 -merging segment 90 into 7 -merging segment 91 into 7 -merging segment 92 into 7 -merging segment 18 into 15 -merging segment 56 into 47 -merging segment 72 into 64 -merging segment 77 into 73 -merging segment 7 into 89 68 defects to be corrected 0 vertices coincident vertex 43773: degenerate normal vertex 88884: degenerate normal vertex 90911: degenerate normal vertex 43773: degenerate normal vertex 88884: degenerate normal vertex 90911: degenerate normal vertex 43773: degenerate normal vertex 88884: degenerate normal vertex 90911: degenerate normal Computing Initial Surface Statistics -face loglikelihood: -9.4721 (-4.7360) -vertex loglikelihood: -7.7263 (-3.8632) -normal dot loglikelihood: -3.5502 (-3.5502) -quad curv loglikelihood: -6.2319 (-3.1159) Total Loglikelihood : -26.9804 CORRECTING DEFECT 0 (vertices=32525, convex hull=4561) Does it look like its frozen? And if so, could I just run autorecon from the fix topology part, so I dont have to re-run the whole thing?

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tesselating
by Chacko Cherian 22 Jun '06

22 Jun '06

Hello all, I ran an Analyze format image in Fresurfer...just the Morphometry and reconstruction tutorial..but found that it's creating a filled.mgz volume but I'm having a problem in tesselating and creating the outputs lh.orig and rh.orig for the left and right hemispheres.It displays a very tiny piece of the volume. Could you please let me know how to troubleshoot this problem.. THanks in advance. Chacko. Chacko Cherian M.S EE Graduate Assistant Department of Psychology Arizona State University. Tempe,AZ. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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nu_correct problem
by tao＠ucsd.edu 22 Jun '06

22 Jun '06

>Hi Bruce: >> >> I installed the new version of freesurfer. I found that nu_correct does >> not work properly, the error message is >> spawn: exec of nu_estimate_np_and_em failed: No such file or directory >> nu_correct: crashed while running nu_estimate_np_and_em (termination >> status=65280) >> >> so I try to execute nu_estimate_np_and_em, and get following message: >> nu_estimate_np_and_em: data directory for package "N3" not found in >> /usr/pubsw/packages/freesurfer/RH3-x86_32/lib/mni/data >> >> Any idea? Thanks in advance. BTW, the GUI can pass that, but there is no >> intensity correction, of course. >> Tao

2 1

aseg error?
by Inge K. Amlien 22 Jun '06

22 Jun '06

As seen in the attached image, voxels outside the pial surface has been labelled as cortex. Will these voxels be included in aseg.stats, or is it normal? mri_ca_register segfaulted during an earlier run, and I restarted it without touching any files, could this have caused it? Regards Inge Amlien University of Oslo (Norway) ----- Freesurfer 3.03 x86_64

2 1

Basic questions
by Anil Roy 21 Jun '06

21 Jun '06

Hello all, I have a few basic questions about FreeSurfer and would appreciate any help. 1) I have a number of brains in mnc format. I was wondering if these could be used in FreeSurfer because the tutorials only mention usage of the mgz format. Also, how do we convert from mnc to mgz. 2) What is the exact method of extracting the volume and cortical thickness of a particular region once the brain has been loaded into freesurfer. I can't seem to find any docs that outline how this is to be done with freesufer. If someone could point me in the right direction it would be really helpful. Thanks a lot, Anil Roy.

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FS-FAST: mkcontrast-sess -setwdelay
by raij＠nmr.mgh.harvard.edu 21 Jun '06

21 Jun '06

Hi, I have a large (~100) number of FIR analyses where I need to set the weights for each post-stimulus delay (and then collapse them with -sumdelays). The weights are the same for all analyses. However the -setwdelay weights can only be entered manually upon prompt. This means that I would have to sit by the computer for a few days just to copy-paste a short series of numbers every 25 min. This makes no sense of course. Is there a way to make feeding the -setwdelay numbers part of the analysis script so I could just let it run without human intervention? I would be very happy if I could just set in the analysis script, for example, mkcontrast-sess -analysis XXX -setwdelay 0 0 0 0 1 1 1 0 0 0 0 0 -sumdelays -contrast A-REST -a 1 -c 0 Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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recon-all without tcsh
by Ajith Kumar U 21 Jun '06

21 Jun '06

Hi, Can recon-all run even if tcsh is not installed on the system. When I try running it, I get the message: -bash: /home/aju/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory Thanks, Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

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tksurfer rendering offscreen
by Don Hagler 21 Jun '06

21 Jun '06

In older versions of tksurfer, it was possible to set a renderoffscreen flag (in a tcl script) that would make it possible to render images in the background. I find this very valuable for rendering large batches of stats. I would like to store surface-painted timeseries data in mgh format and render each frame in order to make a movie. Since the old version of tksurfer will not read mgh files, I need to use the new one for this. But rendering onscreen is very annoying because it means you can't use your computer for hours (if rendering lots of images). The problem seems to be that tksurfer is opening a window and drawing it twice before the tcl script even begins to be interpreted. Is this something that can be fixed? Just in general, why should time be wasted drawing the surface twice upon opening? And can the tcl script be interpreted *before* any open_window or redraw commands are given?

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