Freesurfer July 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
88 discussions

Gray matter volumes
by Derin Cobia 19 Jul '06

19 Jul '06

Hi again, Two questions: 1). You said earlier that GM volumes from mris_anatomical_stats are more accurate than from the aseg files. Would you recommend using the surface-based GM volumes instead of the ones from the aseg.stats files? I ask because we have ~200 subjects processed for volume, but not surface, meaning no mris_anatomical_stats. If we could avoid the added processing time on these it would be helpful, but don't want to do it at the expense of accuracy. 2). What structures are calculated into "total white matter volume" under mris_anatomical_stats? Does it include corpus callosum and others? Thanks. -Derin

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label list for lh.aparc.annot
by R. Chen 19 Jul '06

19 Jul '06

Hi, I use freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 For a subject, in folder ${SUBJECTS_HOME}/label, I can find two annotation file lh.aparc.a2005s.annot lh.aparc.annot In freesufer home, I can find a file surface_labels.txt. It looks like 0 Unknown 0 0 0 0 1 G_cingularis 25 60 60 0 2 G_cuneus 180 20 20 0 3 G_frontalis_inf-pars_opercularis 220 20 100 0 4 G_frontalis_inf-pars_orbitalis 140 60 60 0 5 G_frontalis_inf-pars_triangularis 180 220 140 0 6 G_frontalis_medius 140 100 180 0 7 G_frontalis_sup-pars_lateralis 180 20 140 0 8 G_frontalis_sup-pars_medialis 180 140 100 0 9 G_frontomarginalis 140 20 140 0 10 G_hippocampi 25 180 20 0 My question is whether this file is for lh.aparc.a2005s.annot or lh.aparc.annot? If this contains structure name for lh.aparc.a2005s.annot, where is the corresponding label list file for lh.aparc.annot. Thank you Ron --------------------------------- How low will we go? Check out Yahoo! Messengers low PC-to-Phone call rates.

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recon-all: error in topology correction step
by Johannes Klein 19 Jul '06

19 Jul '06

Hi everyone, I'm using recon-all to flatten a number of scans from patients and controls. Most of them work fine, but there are 3 that do not reconstruct correctly. They all seem to share the same problem: Recon-all aborts during the automatic topology correction step, and there's a line in the log saying mrisDefectAnalysis : defect XXX overlap defect YYY. I've checked registration to talairach, skull strip and initial surfaces, the only thing I could see was that in some cases, bits of the superior sagittal sinus were wrongly included in the lh.orig.nofix, or small bits of dura, but nothing major. I'm attaching the relevant output from the topology fixer for two different cases. I would be grateful if someone could point me at other things to try. Is it possible to visualise the defects' locations, so I could find out which defect is actually causing the overlap message? Thanks for your help everyone, Johannes ---------- CASE 1 #@# Fix Topology lh Wed Jun 14 04:04:29 BST 2006 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_2280 lh \n 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 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-656 (nv=197397, nf=396220, ne=594273, g=329) 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 9 iterations marking ambiguous vertices... 30743 ambiguous faces found in tessellation segmenting defects... defect 6 : 7 vertices have been added to the surface [ ... ] defect 314 : 2 vertices have been added to the surface total of 95 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 277 overlap defect 272 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno6.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Wed Jun 14 04:08:10 BST 2006 CASE 2 #@# Fix Topology rh Thu Jun 15 12:13:05 BST 2006 \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_3509 rh \n 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 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-2025 (nv=252518, nf=509180, ne=763723, g=1013) 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 13 iterations marking ambiguous vertices... 137391 ambiguous faces found in tessellation segmenting defects... defect 12 : 4 vertices have been added to the surface [ ... ] defect 440 : 4 vertices have been added to the surface total of 340 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 395 overlap defect 393 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno4.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Thu Jun 15 12:19:26 BST 2006

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Parcellation and bias field correction
by Mike Chee 19 Jul '06

19 Jul '06

----- Forwarded Message From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Wed, 19 Jul 2006 08:42:08 -0400 (EDT) To: Mike Chee <mchee(a)pacific.net.sg> Hi Mike A. the wm parcellation isn't released yet, but I think we'll do so soon (Doug: what do you think). The current tools should allow you to correlate demographic/neuropsych with parcellation units (e.g. superior frontal gyrus). B. The improved bias correction should help both the cortical and subcortical streams. C. The control points range of effect depends on the other control points (auto and manual) near it). If a control point is anterior to all others it can have an effect on the entire frontal region. you should post these to the list - other people can answer some of them (like A) better than I can. cheers, Bruce On Wed, 19 Jul 2006, Mike Chee wrote: > Hi Bruce, > > I have a couple of questions: > A. We are interested in correlating parcellated brain volumes of brain lobes > (not subcortical structures for openers) with neuropsych test scores. For > example, middle frontal gyrus volume with executive function. Presently, it > seems that it is possible to evaluate cortical thickness globally and then > pick our areas that regress to a significant extent with variables of > interest. At some point in time, it would be good to see if the combination > of GM + the underlying WM would give additional / complimentary information. > In this regard, I am not entirely clear how we are to realize this goal. > According to David’s HBM 2006 poster, this would take place by adding the > volume of the cortical rim and its underlying WM. > B. If so, this would necessitate good quality segmentation along the > volumetric pipeline (that generates the .aseg images). This in turn would > require some adjustments in the segmentation of white matter using the > volume processing stream. By dropping control points, we active improved > segmentation along the surface processing stream (correct?) If so, how are > benefits to volume measurement realized? As I understand our data, the > surface processing pipeline is more or less satisfactory as is. So I wonder > what the marginal benefit of dropping control points is? > C. A final question relates to how laying control points in WM works. Jenni > told us that dropping more points increases intensity in an additive > fashion. If so what is the intensity shift and how extensive is the induced > change? > If you think these questions serve a general audience, feel free to post > this question in the help website. > > Mike > ------ End of Forwarded Message

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Expanding pial outline
by Jake Freimer 18 Jul '06

18 Jul '06

I ran two brains through autorecon2 and the pial line is drawn too close at many parts and cuts off parts of the brain. I looked through the website and only saw instructions for how to remove stuff and make the pial line smaller. I was wondering if there is a command I can run to expand the pial line or what is the best way to edit the files so more brain is included. I was looking at the threshold tools and couldn't see a way to convert say anything with a value of 30-40 to 60, so I was wondering if that was also possible. Thanks -- -Jake

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viewing subcortical structures
by Sasha Wolosin 18 Jul '06

18 Jul '06

Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha 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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Re: [Freesurfer] recon-all error
by Anil Roy 17 Jul '06

17 Jul '06

That could be the case. I start recon-all and just leave the computer for 24 hrs. Is there a way to find out what could be doing this. Anil. On 7/17/06, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > is there some builtin time limit that you are exceeding? The log file just > says: > > mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z > /usr/local/freesurf\ > er/average/RB_all_2006-02-15.gca nu_noneck.mgz > > erasing everything more than 25 mm from possible brain > reading atlas '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... > setting gca type = Normal gca type > reading input volume 'nu.mgz'... > reading transform 'transforms/talairach.m3z'... > Killed > Linux dhcp-129-105-146-221.speech.northwestern.edu 2.4.22-10mdk #1 Thu Sep > 18 1\ > 2:30:58 CEST 2003 i686 unknown unknown GNU/Linux > > recon-all exited with ERRORS at Sat Jul 15 01:11:14 EDT 2006 > > > > which sounds like some other process killed this one. > > Bruc > > On Mon, 17 Jul > 2006, Anil Roy wrote: > > > Hello All, > > > > I've been running recon-all on a couple of minc brains on Fedora Core 4 > and > > everything thing runs fine. I started running a few on a Mandrake > > Linux 9.2system but each time recon-all exits with errors and I'm > > unable to see why. > > I've attached the recon-all.log file and would appreciate any input on > why > > this is occurirng. > > > > Thanks, > > > > Anil Roy. > > >

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Hemispheric devision problem
by Akram Bakkour 17 Jul '06

17 Jul '06

Hi all, I've been having trouble with these two brains with huge ventricles, first the aseg failed, and the ventricles didn't get filled automatically, so I filled them manually and ran recon-all -autorecon2-wm but my surfaces were off and there was a blatant hemispheric devision problem with the surfaces, so I added a corpus callosum seed point using recon-all -autorecon2-wm -cc-crs <X Y Z> but that didn't work. I ran out of fixes to try, any suggestions!? Thanks! On machine blakey source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/banzai/3/users/efenster/CLINDEM_processing/ which mri_convert /usr/local/freesurfer/stable/bin//mri_convert cd $SUBJECTS_DIR recon-all -autorecon2-wm -cc-crs 126 98 97 -subjid 06142006_4TTclindem03 subjid 06142006_4TTclindem03 recon-all -autorecon2-wm -cc-crs 129 113 128 -subjid 06212006_4TTclindem04 subjid 06212006_4TTclindem04 check output: foreach s (06142006_4TTclindem03 06212006_4TTclindem04) tkmedit 06142006_4TTclindem03 lh.white -aux wm.mgz -aux-surface rh.white end Notice the hemispheric devision problem with the surfaces. Any suggestions as to how to fix this!? Thanks! Akram.

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Question concerning orientation
by Jake Freimer 17 Jul '06

17 Jul '06

I have run several instances of autorecon2 and have only got left hemisphere data. The log file says that autorecon finished with errors but I can not find where to find these errors. I believe that the problem is the way the data being fed in is oriented so I was wondering how I should reorient it to get it to work. Thanks Jake

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general question concerning orientation
by Chacko Cherian 17 Jul '06

17 Jul '06

Hello everyone, orientation i guess is quite an issue. Well how does,Freesurfer determine orientation of the image.Do I have to know how the image has been processed before it reaches me or is there any other way to find out?Does it have to do with the 'flip'? I checked the orientation of an image on SPM and on Freesurfer. Left on SPM is Right on Freesurfer and vice versa is what I got. Essentially how do I determine L-R orientation? Thanks in advance, Chacko Cherian. Arizona State University. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Freesurfer July 2006