Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

recon-all with MT images?
by Lucia Garrido 02 Mar '09

02 Mar '09

Dear Freesurfers, I was wondering whether it would be possible to run recon-all with MT images? My final aim is to compare cortical thickness between two groups. I've done this with T1 weighted images, but was wondering whether i could also do with MT images. Segmentation in SPM worked really well on these images. Thank you very much. Best wishes, Lucia

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clusterwise correction for multiple comparisons
by Devdutta W 02 Mar '09

02 Mar '09

Hi, In the mri_glmfit-sim command, when it does a "clusterwise correction" is it correcting across the whole brain? In other words, does the term "clusterwise" mean that it is only correcting within that cluster or is it correcting across the whole brain, cluster-by-cluster (instead of, say, voxel-by-voxel)? While doing this analysis, (after displaying the .annot file in tksurfer as stated in the documentation), I noticed that our display did not match what was shown in the docs. In the documentation, the picture we are supposed to see only displays the clusters (all clusters, regardless of the significance). Ours displayed cortical parcellations in addition to the clusters. This may just be a display issue and the analysis might still be correct, but I just want to be sure. Has anyone else encountered this? Thanks for any light anyone can shed on these questions. Devdutta

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aparc-stats wth curv-file as input?
by Florian Gerstl 02 Mar '09

02 Mar '09

Dear FS-Team, I have mapped some PET-data on the corresponding subject's cortical surface. Is it possible to get some statistics from the resulting curv-file using the FS-parcellation as ROIs? Thanks in advance, Florian

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¿write_annotation?
by Rafa x 02 Mar '09

02 Mar '09

Dear FS team, I used read_annotation(lh.aparca.annot) for obtaining [vertexs, label, colortable]. After that, I have modified these variables and would like to write a new annotation file. Is there the function "write_annotation" (or something similar)? Thanks in advance. Best, Rafa

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Normal vector of length zero
by Pradeep Reddy Ramana 01 Mar '09

01 Mar '09

Hello Freesurfer Experts, I ran into the following error when running Freesurfer for one of our subjects, during: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh I could only find a partial answer to a previous post on a similar problem - pasted at the end. Following that, I looked at lh.orig.nofix surface - screenshots attached. I am not sure whether its alright. No rh surfaces were created. Please let me know how to correct this problem and proceed further. Quick response will be greatly appreciated, Pradeep ======= Tail end of scripts/recon-all.log ========== #-------------------------------------------- #@# Fix Topology lh Fri Feb 27 19:29:56 PST 2009 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly 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 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.10 2008/03/10 13:59:45 nicks Exp $ before topology correction, eno=-264 (nv=105340, nf=211208, ne=316812, g=133) 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 8 iterations marking ambiguous vertices... 45195 ambiguous faces found in tessellation segmenting defects... 81 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 0 -merging segment 7 into 0 -merging segment 0 into 18 -merging segment 39 into 28 -merging segment 37 into 30 -merging segment 54 into 46 -merging segment 53 into 59 -merging segment 72 into 64 -merging segment 71 into 70 72 defects to be corrected 0 vertices coincident reading input surface /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2008 (-4.6004) -vertex loglikelihood: -6.9827 (-3.4913) -normal dot loglikelihood: -3.5884 (-3.5884) -quad curv loglikelihood: -6.0560 (-3.0280) Total Loglikelihood : -25.8279 CORRECTING DEFECT 0 (vertices=73, convex hull=66) After retessellation of defect 0, euler #=-61 (80515,236855,156279) : difference with theory (-69) = -8 CORRECTING DEFECT 1 (vertices=212, convex hull=29) After retessellation of defect 1, euler #=-60 (80531,236912,156321) : difference with theory (-68) = -8 CORRECTING DEFECT 2 (vertices=14, convex hull=24) After retessellation of defect 2, euler #=-59 (80534,236928,156335) : difference with theory (-67) = -8 CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory Linux ilpc9.cs.sfu.ca 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Feb 27 21:07:28 PST 2009 ======================================== ------------------ Previous post with a similar problem ------------------- [Freesurfer] Problem with latest dev version (crashes correcting errors) Tim Jarvis jarv0075 at umn.edu Mon Feb 6 12:41:21 EST 2006 * Previous message: [Freesurfer] Problem with latest dev version (crashes correcting errors) * Next message: [Freesurfer] Problem with latest dev version (crashes correctingerrors) * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] For the lh, there is no cerebellum and no skull, looks to be correct. I don't see any rh* files though? brewster 14%> ls /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ lh.defect_borders lh.defect_chull lh.defect_labels lh.inflated lh.inflated.nofix lh.orig lh.orig.nofix lh.qsphere.nofix lh.smoothwm.nofix On 6 Feb 2006, Bruce Fischl wrote: > yes, mri_ca_register takes a long time. The good news is it works really > well :>. As for the mris_topology_fixing problem, what does the > ?h.orig.nofix surface look like? Does it include cerebellum or skull? Does > it look approximately correct? > > On Mon, 6 Feb 2006, Tim Jarvis wrote: > > > Gave the new dev version a spin with autorecon-all, couple of things... > > > > For the mri_ca_register step, it took a total of 791 minutes! Is this > > normal or could this be a hint as to things going wrong early in the > > pipeline? > > > > Also, the program eventually crashed during the error correction, below are > > the lines that seem like they may have had some effect: > > > > Anyone else experience this problem? > > > > > > > > Thanks > > -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 Freedom from the desire for an answer is essential to the understanding of a problem - Jiddu Krishnamurti

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effect sizes and SE
by Lars M. Rimol 01 Mar '09

01 Mar '09

Hi, Is there a way to get the standard error of the adjusted means for each group in a glm with a categorical predictor? -- yours, LMR

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scale axis range
by Juranek, Jenifer 27 Feb '09

27 Feb '09

Hi, Running fsv4.2.0 on RHEL4. Within qdec, the "graph average ROI" provides valuable information in scatterplot format. Is it possible for users to define the axis range (especially the Y-axis)? For some unknown reason, we have encountered several instances where data points are not displayed since the scale range of the automatic plot does not capture the entire range of individual subject data. Restarting qdec, re-running the design, and reloading the label does not alter the outcome. Any thoughts or quick fixes?

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Re: tksurfer display problems vary by OS version
by David Mischel 27 Feb '09

27 Feb '09

Hello, everyone. I received a very nice note from Siddharth Srivastava in response to my initial post. Unfortunately, his suggestion (shared library load order) did not have any effect. On a closer look I see that the tksurfer script, which calls tksurfer.bin, already ensures that the correct FS TCL library path is put first in the share library load order. Since the same script is executing the same code on different operating systems I am still thinking that some variant in the system libraries for rendering are part of the problem. Can anyone using a CentOS 5 host for tksurfer confirm whether it is correctly displaying whole brain images? I would appreciate getting a positive case report. Thanks, < david > Message: 7 > Date: Thu, 26 Feb 2009 13:48:34 -0800 > From: David Mischel <David.Mischel(a)ucsf.edu> > Subject: [Freesurfer] tksurfer display problems vary by OS version > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <49A70E32.1070409(a)ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, everyone. > > I just joined this list in order to post a problem our folks are having > with tksurfer displaying brain images. What we are seeing is incorrect > display of images depending on what OS tksurfer is run on. In one case, > the image is never rendered because some kind of error loop is > triggered. In all test cases the same data and Freesurfer version are > being used (4.0.1) and the same display hardware and software are being > used. The only difference is the host OS running tksurfer. > > Here's what we are seeing: > > Operating system Result > > Fedora Core 4 (32 bit) Success > > Fedora Core 5 (64 bit) Failure (run away X errors) > > Cent OS 5 (64 bit) Failure (incorrect image) > > ... > Message: 8 Date: Thu, 26 Feb 2009 13:58:36 -0800 From: Siddharth > Srivastava <siddys(a)gmail.com> Subject: Re: [Freesurfer] tksurfer > display problems vary by OS version To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <d440b0e10902261358q12704d8dn7468867e98c99a6f(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" Hi david, I dont know > if this will help, and i really do not know the reason why it should > work, but if you append the tcltktixbli/lib, /usr/lib and /usr/lib64 > on 64 bit version *in this order*, the tksurfer problems are solved. ... -- David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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Freesurfer Downloading Problem
by Naveen Kumar Yadav, Mr 27 Feb '09

27 Feb '09

Hi Nick, Thanks for your previous reply. But I still have some questions. 1. Do I need to Uninstall the Freesurfer software that I already installed with LINUX Platform Red Hat9. If I need to Uninstall it then what UNIX command I need to use so that I'll not delete some other files. 2. In your previous reply you asked me to Install the Freesurfer software with Platform CentOS4. So, Do I need to install the one with Platform CentOS 4 or with Platform CentOS 4 X 86_64. I did check that I have latest version of Redhat in my computer i.e. rh(el)5. Please reply to me. I'll be thankful to you. Thanks Regards Naveen K. Yadav MSc Research Assistant Dept. of Ophthalmology McGill Vision Research McGill University Montreal, Quebec, Canada -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 2/25/2009 12:29 PM To: Naveen Kumar Yadav, Mr Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Freesurfer Problem Naveen, I would try the freesurfer centos4 distribution. Despite the numbering, rh9 is very old, and rh(el)5 is newish. Also, can you report back to me if you have any problems with the download? We've had some problems reported lately with slow or error prone downloads from our site. Nick On Wed, 2009-02-25 at 11:58 -0500, Naveen Kumar Yadav, Mr wrote: > Hi, > > I used Linux Red Hat 5 to install the freesurfer from your website. I followed the downloading and Installing steps as mentioned in your website. > > But when I tried to Test the Freesurfer Instalation it gave me the following message > > [inverse@localhost subjects]# tkmedit bert orig.mgz > tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory. > > So I am wondering does it make difference if we download the latest Freesurfer software on Redhat 5 or Redhat 9. Is the error is due to linux version or is there is anyother problem. > > We used this Unix command to download the sofware on Redhat 5 > > ...freesurfer-Linux-rh9-stable-pub-v4.2.0.... > > Please let me know the solution. I will be thankful to you. > > Thanks > > Regards > > Naveen K. Yadav MSc > Research Assistant > Dept. of Ophthalmology > McGill Vision Research > McGill University > Montreal, Quebec, Canada > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Scale factor
by Rafa x 27 Feb '09

27 Feb '09

Dear FS team, I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer release is 4.2 Thanks in advance for your help. Best, Rafa

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