Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

Segmentation optimization
by Joao Pereira 26 Jun '06

26 Jun '06

Hello again, I've been having some problems with FS segmentation, especially around the temporal lobes, where there is a clear underestimation of the pial surface (and manual edits are not being too successful). The problem is clearly related to the poor resolution of the used images. Are there any parameters to change in order to optimise the segmentation process? Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else? Thank you again. Joao Pereira

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recon-all error
by Anil Roy 25 Jun '06

25 Jun '06

Hello All, So I tried using recon-all to get a few parcellations stats from a minc file it but I'm getting the following error. Please could someone say how this can be rectified. Thanks. - Anil Roy. This is the command I'm giving: # recon-all -force -i /root/Desktop/F100.mnc -subjid F100 -sd /usr/local/freesurfer/subjects -autorecon3 This is the output. INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: /usr/local/freesurfer/subjects/F100 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 30123 Jun 23 15:50 /usr/local/freesurfer/subjects/F100/scripts/recon-all.log Linux dhcp-129-105-146-155.speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux WM removal version /usr/local/freesurfer/subjects/F100 mri_convert /root/Desktop/F100.mnc /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz mri_convert /root/Desktop/F100.mnc /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz reading from /root/Desktop/F100.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/F100/mri/orig/001.mgz... #-------------------------------------------- #@# Sphere lh Fri Jun 23 15:56:29 CDT 2006 /usr/local/freesurfer/subjects/F100/scripts mris_sphere ../surf/lh.inflated ../surf/lh.sphere $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ $Id: mrisurf.c,v 1.441.2.3 2006/04/12 02:03:02 nicks Exp $ MRISread(../surf/lh.inflated): could not open file No such file or directory mris_sphere: could not read surface file ../surf/lh.inflated No such file or directory Linux speech.northwestern.edu 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Jun 23 15:56:29 CDT 2006

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Re: [Freesurfer] The "5 mm limit" on cortical thickness?
by Graham Wideman 23 Jun '06

23 Jun '06

At 6/23/2006 06:57 PM, you wrote: >probably not. Check the intensity of the white matter underlying the gray >and see if it's significantly less than 110. If so, try putting a few >control points there (make sure they aren't in partial-volumed wm) Bruce: You would recommend this, even though the white boundary looks more or less in the right place? One incongruity is that the aseg segmentation gets the grey pretty much right, but the pial surface is way inboard. (I do understand that the aseg grey is not used to find the surface, it just *looks* like it should be smarter!). And probably we shouldn't strain this discussion too far at this point... we need to take a closer look given that the "5 mm" hypothesis is thrown out... Graham

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Re: [Freesurfer] The "5 mm limit" on cortical thickness?
by Graham Wideman 23 Jun '06

23 Jun '06

Bruce: Thanks for your reply -- >actually the limit is in the thickness measurement, not the deformation. >You can recreate the thickness files with mris_thickness -max $maxthick ... >if you want a larger value. What's going wrong? Well we're trying to guess why the pial surface is somewhat consistently (across subjects) positioned short of the actual pial surface in certain instances, notably frontal medial temporal, and some other locations. We had wondered whether it was because of such a limit. Graham

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The "5 mm limit" on cortical thickness?
by Graham Wideman 23 Jun '06

23 Jun '06

Probably Nick or Bruce: Could you confirm what I think I remember: that in the algorithm to move the surface out from the white position to the pial, FS is constrained by a 5 mm limit? -- Is this documented somewhere, with other details like what unwanted behavior this prevented, in what regions? -- Can this be disabled or set to a different value using a variable or somesuch? Thanks, Graham

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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

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Freesurfer June 2006