Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

volume difference in aparc.stats and wmparc.stats
by Guang Zeng 05 Oct '09

05 Oct '09

Hi, there, I am looking at the volume size of front pole . In lh.aparc.stats, this volume is 590, while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610, which one is accurate? Thanks a lot! BTW: In FreeSurfer Tutorial : Process Flow (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) The follwing command is called at the end of recon-all -autorecon2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 006_S_0547_20070924 --surf-wm-vol --ctab /home/m047599/freesurfer-install/freesurfer/ASegStatsLUT.txt However, when I looked at the recon-all.log file, it is called at the very end of autorecon3, am I right? Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/

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images with poor resolution
by Dana W. Moore 05 Oct '09

05 Oct '09

Hi everyone, I am trying to salvage some images that were done with poor gray/white boundary contrasts. First, FreeSurfer includes an area of dura in the skull strip. I tried adjusting the watershed but it made no differences. FreeSurfer is subsequently unable to detect the gray/white boundary and labels the dura as cortex: [] Looking at the raw images, the gray/white boundaries are faint but visible. Is there anything I can adjust to try to make this work with FreeSurfer? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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WM surface errors
by Alex Fornito 05 Oct '09

05 Oct '09

Hi, I am trying to reconstruct the surfaces of some 1.5T images that I have. For a subset of images, portions of the white matter surface in the occipital cortex are missed, even though the wm.mgz volume seems to have segmented the area correctly. The aseg also seems to have labelled this region correctly (e.g., it is not labelled erroneously as ventricle). I have tried using control points, but this had little impact on the final solution. I've attached pics of the surfaces on the anatomical and wm volumes, along with the locations of the control points so you can see for yourself (note that I placed control points on consecutive slices through the areas). Any advice on how I can fix this problem? Thanks, Alex

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white matter parcellation
by Dana W. Moore 02 Oct '09

02 Oct '09

Hi everyone, I was wondering what atlas the white matter parcellation is based on, and if there is an article that describes it. I have articles for the cortical parcellation and subcortical segmentations, but not the white matter segmentation. One particular question I have regarding the parcellation is why there are large areas of unsegmented white matter. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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mri_convert resample
by Satrajit Ghosh 02 Oct '09

02 Oct '09

can i use mri_convert to resample a 4-d nifti volume? currently it appears to write out just one frame. cmdline used: mri_convert -vs 2 2 2 r234000-20-1_warped.nii r234000-20-1_warped_fsresample.nii the input volume has 51 timepoints the output vol has 1. would you recommend another, more appropriate function? cheers, satra

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Segmentation fault when making base subject for longitudinal processing.
by Hui Zheng 02 Oct '09

02 Oct '09

Hi Nick, For one of our subjects, during the processing of base subject, I encountered this segmentation fault error at the stage of WM segmentation. Here's the output from the pipeline. #@# WM Segmentation Thu Oct 1 15:08:16 SGT 2009 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.3 +- 7.3 [80.0 --> 125.0] GM (74.0) : 72.5 +- 10.2 [30.0 --> 96.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 92.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 1078 sparsely connected voxels removed... thickening thin strands.... Segmentation fault (core dumped) Linux neuron02 2.6.9-42.ELsmp #1 SMP Tue Aug 15 10:35:26 BST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 1 15:09:04 SGT 2009 I have restarted the processing several times, every time it stopped with same error. I can upload the data if needed. Cheers, Zheng Hui

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Finishing WMParc
by Andrew Jahn 02 Oct '09

02 Oct '09

Hello, I recently ran a batch file on several subjects, but set a time limit which prevented some of them from finishing all the steps of recon-all. In the recon-all-status.log for some of them, the last line is "WMParc". I was unable to find which option of recon-all would do only this step; should I just rerun them with autorecon3? Thanks, -Andy

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regression models in Freesurfer
by Jose Luis Cantero Lorente 02 Oct '09

02 Oct '09

Hi there, I am interested in correlate hippocampus volume (obtained with Freesurfer) with performance in several cognitive task, but have several basic questions: 1. Is it feasible to perform these correlations by using Freesurfer? 2. If so, how could be elimitated (by regression models) the effects of total cerebral volume and intracraneal volume, separately? 3. I would be interested to use a multiple regression model. Is there any wiki page to follow this statistical approach with Freesurfer? Thanks a lot for your help. Best regards, --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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How to calculate differences using the longitudinal data
by Weisinger, Brian (NIH/OD) [E] 01 Oct '09

01 Oct '09

I have run the longitudinal stream on the scans I need, but now I am not sure what to use to compare the differences. If someone could clarify this for me I would really appreciate it. Thanks

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RES: R:Re: Re: problem display tksurfer in vmware
by Pedro Paulo de Magalhaes Oliveira Jr 01 Oct '09

01 Oct '09

The sudo password is brain2009 with this information you can succesfully install FSL using that procedure. Cheers PPJ -- Enviado do meu celular Nokia E71 -----Msg original----- De: giacomo.mandru(a)gmail.com Enviado: 01/10/2009 07:00:09 Assunto: R:Re: Re: [Freesurfer] problem display tksurfer in vmware Hi, I have another question: Can I install FSL on the Ubuntu of VirtualBox to work FS and FSL together? How? I follow the istruction of this site: http://neuro.debian.net/pkgs/fsl.html I add web site on source.list but I ottenied an error when I type: sudo apt-get update. thank you for your patience! best wishes Giacomo Mandruzzato Il giorno 28/set/2009 14.52, Giacomo Mandruzzato <giacomo.mandru(a)gmail.com> ha scritto: > ok.thank for interest. I resolved my problem: > -I installed Virtual Box > -tksurfer: I need to DISABILITATED 3D accelerator graphic in > configuration video of virtual box > -qdec:reboot in kernel configuration, overwrite password for > user 'freesurfer', and so I can create link for libtiff.so.4 named > libtiff.so.3 > Now run correctly, I have to wait about 1 second every rotation for > tksurfer with subject bert , but I think it so good. > thank you very much for your answer > 2009/9/28 Pedro Paulo de Magalhães Oliveira Junior ppj(a)netfilter.com.br> > Have you installed the VirtualBox that comes from the FreeSurfer Wiki? > VirtualBox 3.x? > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.2 www.Netfilter.com.br > --- Novo Netfilter Small Business > 2009/9/28 Giacomo Mandruzzato giacomo.mandru(a)gmail.com> > Hi, > now I have installed Virtual Box with freesurfer, but I have same problem > with tksurfer and a library problem with qdec (it can't find libtiff.so.3 > file, and in the folder I see only libtiff.so.3 file!) > Giacomo > 2009/9/26 Giacomo Mandruzzato giacomo.mandru(a)gmail.com> > thankyou for your help and your rapid answer. > I use bash and i set doublebufferflag=1 but the problem persists! > 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr ppj(a)netfilter.com.br> > In csh use setenv doublebufferflag 1 > In bash export doublebufferflag=1 > -- > Enviado do meu celular Nokia E71 > -----Msg original----- > De: Giacomo Mandruzzato > Enviado: 26/09/2009 09:33:26 > Para: ppj(a)netfilter.com.br > Assunto: Re: [Freesurfer] problem display tksurfer in vmware > Yes, I know but I have problem with VirtualBox in the first boot that I > do! > Can I use freesurfer (and so tksurfer) with vmware? Or Is there any > solution > for my problem? > thank you > 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr ppj(a)netfilter.com.br> > > Use the official FreeSurfer distribution for Virtualbox > > > > -- > > Enviado do meu celular Nokia E71 > > -----Msg original----- > > De: Giacomo Mandruzzato > > Enviado: 26/09/2009 08:22:55 > > Para: freesurfer(a)nmr.mgh.harvard.edu > > Assunto: [Freesurfer] problem display tksurfer in vmware > > > > Hi, > > I'm Giacomo Mandruzzato, a student of Bioengineering at Padova (DIE) and > > I'm > > working on my Thesis with Freesurfer (last version). I am using a > virtual > > machine Vmware 2.5.3 with Cent0S 5.1 running FSL virtual disk in Windows > > Vista Home premium, > > I installed freesurfer and tkmedit e qdec run correctly but when run > > tksurfer (ie tksurfer bert rh pial, like website suggests) display an > > error : > > > > > > > [root@localhost ~]# tksurfer bert rh pial > > > surfer: current subjects dir: /usr/local/freesurfer/subjects > > > surfer: not in "scripts" dir ==> using cwd for session root > > > surfer: session root data dir ($session) set to: > > > > > > surfer: /root > > > surfer: all rgb files written to /root > > > surfer: Reading header info from /usr/local/freesurfer/ > > subjects/bert/mri/T1.mgz > > > surfer: vertices=131860, faces=263716 > > > > > > > > > WARNING: No colortable found! > > > > > > > > > > > > surfer: single buffered window > > > surfer: tkoInitWindow(bert) > > > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl > > > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl > > > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl > > > > > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl > > > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl > > > Successfully parsed tksurfer.tcl > > > reading white matter vertex locations... > > > % > > > > > > > > > > Tksurfer open and I can see only a little piece of brain. > > I have update the video card's driver and I tried to use another vm, > like > > VirtualBox but I left the idea because I found some problem with boot of > > it. > > I have found a similar problem in internet, but without solution: > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html(I > > am not using a Nvidia video card). > > > > > > characteristic of my notebook: > > Olidata , Intel core duo T2450 @ 2 x 2.00 Ghz, > > Ram 2 GB, Windows Vista Home Premium 32bit SP2 updated. > > Video card: Mobile Intel 945 Express Chipset Family > > > > I apologize for bad English and little knowledge of Unix OS. > > Please, if somebody can help I am grateful. > > > > Best Regards, > > > > Giacomo Mandruzzato > > giacomo.mandru(a)gmail.com > > > >

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Freesurfer October 2009