Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

temporal lobe segmentation
by Seyed Shahab Sharifi 03 Jun '09

03 Jun '09

Hi all, I am interested in automated segmentation of temporal lobe using freesurfer. I understand that it is possible to add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. But I am not sure about the practicality of this approach for two reasons; first if all the regions of a temporal lobe can be labeled by Free Surfer, second because I am thinking that the most medial border of the superior temporal lobe could be my arbitrary cut off point of segmenting the temporal lobe, what anatomical/imaging feature has been defined for Free Surfer that distinguishes the white matter of the superior temporal lobe from the stem of temporal lobe (or say putamen) . I would appreciate a response asap. cheers Shahab _________________________________________________________________ Get the best of MSN on your mobile http://clk.atdmt.com/UKM/go/147991039/direct/01/

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Re: [Freesurfer] mkhaedsurf error
by raka maitra 03 Jun '09

03 Jun '09

Hi To check the version of FS If you are usinfg a tcsh shell then use the following commandsource $FREESURFER_HOME/SetUpFreeSurfer.csh If you're using sh shell then useexport FREESURFER_HOME=/Applications/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.sh bestRaka --- On Wed, 6/3/09, SHRIKANTH KULASHEKHAR <contactshriks(a)yahoo.co.in> wrote: From: SHRIKANTH KULASHEKHAR <contactshriks(a)yahoo.co.in> Subject: Re: [Freesurfer] mkhaedsurf error To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Date: Wednesday, June 3, 2009, 4:27 AM Hi, > What's in T1-neuromag/slices? Just an error.log file. > What version are you using? I am not aware of the version of the FreeSurfer. How can I check the version ? Shriks SHRIKANTH KULASHEKHAR wrote: > Hi all, > > When I attempt to create a high-resolution head surface tessellation using mkheadsurf, I end up with the following errors: > > For " mkheadsurf -subjid xxx" the error: cannot find volume T1 for xxx > > or for > > [root@localhost bem]# mkheadsurf -subjid xxx -srcvol T1-neuromag/slices > INFO: log file is /usr/local/freesurfer/subjects/xxx/scripts/mkheadsurf.log > -------------------------------- > Wed May 6 01:03:46 EEST 2009 > /usr/local/freesurfer/subjects/xxx/bem > mri_seghead --invol /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices --outvol /usr/local/freesurfer/subjects/xxx/mri/seghead --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2 > -------------------------------- > input volume: /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices > output volume: /usr/local/freesurfer/subjects/xxx/mri/seghead > threshold1: 20 > threshold2: 20 > nhitsmin: 2 > fill value: 255 > Loading input volume > corRead(): can't open file /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices/COR-.info > ERROR: could not read /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices > ERROR: mri_seghead > > Any advice on what could be wrong ? > > Thanks in advance > > shriks > > ------------------------------------------------------------------------ > Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! <http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting From Chandigarh to Chennai - find friends all over India. Click here. -----Inline Attachment Follows----- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mkhaedsurf error
by SHRIKANTH KULASHEKHAR 03 Jun '09

03 Jun '09

Hi all, When I attempt to create a high-resolution head surface tessellation using mkheadsurf, I end up with the following errors: For " mkheadsurf -subjid xxx" the error: cannot find volume T1 for xxx or for [root@localhost bem]# mkheadsurf -subjid xxx -srcvol T1-neuromag/slices INFO: log file is /usr/local/freesurfer/subjects/xxx/scripts/mkheadsurf.log -------------------------------- Wed May 6 01:03:46 EEST 2009 /usr/local/freesurfer/subjects/xxx/bem mri_seghead --invol /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices --outvol /usr/local/freesurfer/subjects/xxx/mri/seghead --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2 -------------------------------- input volume: /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices output volume: /usr/local/freesurfer/subjects/xxx/mri/seghead threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 255 Loading input volume corRead(): can't open file /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices/COR-.info ERROR: could not read /usr/local/freesurfer/subjects/xxx/mri/T1-neuromag/slices ERROR: mri_seghead Any advice on what could be wrong ? Thanks in advance shriks Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/

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Re: [Freesurfer] changing psubmit to qsub in rebuild script
by Nick Schmansky 02 Jun '09

02 Jun '09

Kevin, The flags "-l nodes=1:opteron –m $USER" included with the pbsubmit command are not necessary to run the rebuild_gca_atlas.csh script. The first just selects nodes with Opteron processors (which happen to be the faster processors in our cluster) and the second just emails the user of the submission. So just submit whatever is in the '$cmd' var to qsub. Nick On Mon, 2009-06-01 at 12:29 -0700, Kevin Scheibel wrote: > Hey All, > > > > The cluster that I submit jobs to uses qsub instead of psubmit, but > I’m trying to preserve the way that rebuild_gca_atlas.csh runs. Here > is the man page for qsub: > > > > http://gridengine.sunsource.net/nonav/source/browse/~checkout~/gridengine/d… > > > > I guess I’m looking for the equivalent of psubmit’s configuration > settings in qsub. I.e. how would I write the following homologous > command in qsub?: > > > > psubmit -l nodes=1:opteron –m $USER -c “$cmd” > > > > Kevin Scheibel > > k.scheibel(a)ucla.edu > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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cluster correction - time to finish?
by Dankner, Nathan (NIH/NIMH) [F] 02 Jun '09

02 Jun '09

Hi all, I have started working with clusterwise correction, and initially attempted to run the mri_glmfit mc-z script with 6000 iterations. After two weeks it still wasn't finished, so I stopped it, and as a test ran the script with 100 iterations to see how long it would take. It still took several days. Processing power is not an issue here, so I was wondering how long the script should take to run the desired amount of iterations (>5000). Thanks, Nathan

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Still not clear about average curvature
by Zhangyuanchao 02 Jun '09

02 Jun '09

I am still not quite clear about the averaging of curvature. Sorry about that. could you tell me exactly which function I should use, and How should I choose each parameter? First, I get the curvature value of the pial surface, I think I should average the curvature value on the pial surface, perhaps not on white surface, I read help, It seems that It is smoothed on the white surface. How shoud I use the pial to smooth. And I want to keep format of the output file same to the lh.pial.H.crv , and the only difference is the scalar value is smoothed. Second, I want to obtain the absolute value of the scalar, In this step I will launch "mri_calc". Third, I want to resample and smooth it using kernel fwhm 20mm. Thanks! yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Segmentation fault during -cortribbon flag in autorecon2
by Andreas Engvig 02 Jun '09

02 Jun '09

Hi, We've been encountering the following error when re-running 43 healthy subjects through both the recon-all -all stream and through the recon-all -long stream. The error seem to occur quite random with regards to the subjects: " #@# Cortical ribbon mask Tue Jun 2 03:09:13 CEST 2009 /work/220791.d/2039B.long.2039A/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2039B.long.2039A SUBJECTS_DIR is /work/220791.d WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. Segmentation fault " We've used Freesurfer v.4.1. The scans have previously been run in fs. 4.05. After the error occurs, I've tried to rerun the subjects just through this step. They usually complete the step after 1-2 subsequent reruns. However, this is quite time consuming - any suggestions how to solve this? We use centOS4 64bit. I run the subjects on our computing cluster which allocates 2,1 GB of memory for each subject. I've seen the error addressed on the list earlier, but I couldn't find any obvious solution. Thanks! Best regards Andreas Engvig Center for the Study of Human Cognition University of Oslo PB 1094 Blindern 0317 Oslo Cell: +47 988 58 770

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smoothing sulc
by qwfy1234567 02 Jun '09

02 Jun '09

Hi, I want to use sulc measure to make group analysis, before making analysis,I have to smooth the sulc measure. Should I smooth it directly or I first get the absolute value,then I smooth it? you know sulc has both positive and negative value? Best, Gang

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-- ROI label map activation
by Suarez, Ralph O., 01 Jun '09

01 Jun '09

Hello all, I am interested in doing ROI analysis of MEG activation using the standard Freesurfer atlas labels. My goal is to quantify the amount of MEG activation in a specific ROI for comparisons between other ROIs, and other subjects. So, ultimately I need to extract quantifiable MEG activation exclusive to a given atlas region. I am a bit confused as how this can be done. Can anyone point me in the right direction? Any suggestion or advice that anyone is willing to offer would be greatly appreciated. Thanks, Ralph

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Option --fwhm with command mri_nu_correct.mni
by Ed Gronenschild 01 Jun '09

01 Jun '09

Hi I tried to use option --fwhm 0.1 with mri_nu_correct.mni and noticed that this is incorrectly interpreted as option --distance 0.1. This script reads if($#FWHM) set cmd = ($cmd -distance $FWHM); whereas this should be if($#FWHM) set cmd = ($cmd -fwhm $FWHM); Is it possible to correct the mri_nu_correct.mni script? Ed

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Freesurfer June 2009