Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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Aparcstats question
by Nathan Dankner 12 Mar '09

12 Mar '09

I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure? Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance, Nathan

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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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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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Work flow for analyzing the data from children
by Xiangchuan Chen 26 Feb '09

26 Feb '09

Dear FreeSurfer experts, I am going to run surface reconstruction on the data collected from children (12-15 years old). Are there any special concerns / options for the work flow in this case? As I guess FreeSurfer might be optimized for analyzing adult brains, I would like to be clear of any issues before starting the work flow for over 80 subjects. Thanks in advance, Xiangchuan Chen

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tksurfer display problems vary by OS version
by David Mischel 26 Feb '09

26 Feb '09

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) I am wondering whether anyone else has seen this problem with this particular program? I'll happily provide as much information as I can to any request for further details. I have some images of the correct and incorrect displays but I'm not sure whether I can post attachments to this list. I can certainly provide them directly to anyone who would like to see what we are seeing. Thanks for your help. < david -- 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 February 2009