Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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

2 1

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

2 1

about segmentation
by Silvia biopanda 26 Feb '09

26 Feb '09

Hi, we are making changes in the aseg.mgz and we need to know how to erase a wrong pixels. we read in the tutorial that the button three erases, but it doesn't work.how can we do? cheers, SK

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Processing leaving out certain processing steps
by Lucas Eggert 26 Feb '09

26 Feb '09

Dear Experts, I would like to compare different processing procedures for the classification of gray matter. For this purpose, I would like to compare e.g. FreeSurfers default processing stream for subcortical labeling with the result that you get, if you leave out bias correction (nu_correct) in this processing pipeline, or replace N3 with another bias-correction algorithm. But, it appears to me, that the subsequent steps always look for the output-file of the previous processing step that would have took place in the default processing. So, my question is: How can I most efficiently leave out or replace single processing steps in FreeSurfer's default processing stream? Any help would be very much appreciated. All the best, -Lucas _______________________________________________________________________ DSL zum Nulltarif + 20 Euro Extraprämie bei Online-Bestellung über die DSL Freundschaftswerbung! http://dsl.web.de/?ac=OM.AD.AD008K15279B7069a

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standard error for betas
by Lars M. Rimol 26 Feb '09

26 Feb '09

Hi, I have fitted a glm with three different groups, using mri_glmfit (FS v4.0.3). I use the beta.mgh to get the adjusted means within an ROI, for each group. I'd like to make a bar or box diagram with the adjusted means/betas, but I'm not sure how to get the standard error of the betas so I can make error bars or a confidence interval. It seems that mris_anatomical_stats won't take the beta.mgh as input. Is there another way to do this in FS? Or will I have to do it outside FS? All my contrasts have only one vector, so each comparison should reduce to a t-test (according to the Wiki). In general, given the p (sig.mgh) and df of a t-test, I can get the t-value, and given the difference between the betas, the df and the t, I can get the SE. But I assume this is a little more complicated than that? I guess I can't use the rvar.mgh or rstd.mgh, since these are based on the whole model and not just the two groups. Which brings me to a related question: In mri_glmfit, when you have more than two groups in your model, and perhaps also e.g. age as a continuous regressor, and you set a contrast to compare two of the groups, does the variance estimate (SE) include the variance of all the variables, i.e. all groups that are in the model including the ones not included in the comparison + whatever covariates there may be? If so, isn't it really closer to a Tukey's or Scheffe's than an ordinary t-test? But back to my main question: Is there a way to get a measure of dispersion or confidence for the betas associated with each of the three groups in my analysis? (And if there is, I probably can't just average that measure across all vertices in the ROI, right?) Thank you! -- yours, LMR

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creating an infodump.dat file
by Dominique Jennings 25 Feb '09

25 Feb '09

Hi, I am trying to determine the b-values, number of directions and b0 volumes in a GE DTI data set. I know that unpackdcmdir creates an infodump.dat file, and that one can obtain these parameters from that file. I am using a slightly modified version of the 'dcmdir-info-ge' script (written by Doug Greve), but it doesn't automatically create an infodump file (at least, not yet). I would like to create a similar infodump file for these GE data. Does someone out there know how 'unpacksdcmdir' makes that infodump.dat file? Thanks in advance. Nicki

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Thickness histogram on labelled region only
by Pierson, Ronald K 25 Feb '09

25 Feb '09

I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and significant regions that are zero) that may be creating some interesting cingulate results we are seeing. I see there is a matlab script to look at the thickness histogram of the entire cortex, but is there a way to create a histogram for just one labeled region at a time? Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

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