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30080 discussions

qdec error finding files
by Mischka Gerken 24 Mar '08

24 Mar '08

Hello to all the kind people at FreeSurfer! We are having difficulty running qdec. After solving my issues loading tables, qdec is having difficulty loading certain files. Our current error is that qdec says it cannot find the lh.curv file for the fsaverage subject. -I have verified that this file exists, and that it exists in the proper location (same directory qdec indicates it is searching in) -we have exported the correct subjects directory (in BASH not TCSH) -everything else until that point seems to be ok. We have been able to run some analysis just fine, then others run into this error of not being able to find files (no clear pattern why, but very frequent). This is a very simple trial (11subjects in two groups, so just one discrete variable). We have made the average subject (exited without errors) We have run -qcache on all subjects very recently (2 days before analysis) Any thoughts on what we might be doing wrong? -Mischka

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libXmu error on cluster
by Pedro Paulo Oliveira Jr 24 Mar '08

24 Mar '08

Hi, I ran 40 process and all finished with /b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon-all.log:mri s_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory But in /usr/lib there is a libXmu.so.6 My questions are: 1) Anybody know why it failed? 2) If I fix this how can I run recon-all from this point? Thanks PPJ

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Error on Spline Cubic Set
by Pedro Paulo Oliveira Jr 21 Mar '08

21 Mar '08

Anyone can shed a light? FS 4.0.2 i386 CentOS Fri Mar 21 20:11:45 EDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Fri Mar 21 20:11:46 EDT 2008 /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2855, pval=0.0254 >= threshold=0.0050) awk -f /b/03/netfi01/freesurfer/bin/extract_talairach_avi_QA.awk /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri/transforms/talairach_av i.log TalAviQA: 0.97187 z-score: -1 #-------------------------------------------- #@# Intensity Normalization Fri Mar 21 20:11:46 EDT 2008 /b/03/netfi01/freesurfer/subjects/neliseoliveira/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.157 0.025 -0.069 -0.036; 0.081 0.971 0.642 1.728; 0.091 -0.685 1.159 -15.320; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. Linux n122128 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:54:20 EDT 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Fri Mar 21 20:11:51 EDT 2008

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visualizing individual structures
by Thomas Thesen 21 Mar '08

21 Mar '08

Hi All, What is a good and straight-forward way to visualize individual structures based on the segmentation (e.g. hippocampus) and labels (e.g. aparc)? Is that possible with the Freesurfer tools? cheers, Thomas --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

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obtaining older version of freesurfer
by Glenn Lawyer 21 Mar '08

21 Mar '08

Dear FreeSurfer team, Do you still make older versions of FreeSurfer available on your website? I'm specifically looking for a v3 stable release, but my situation may not be unique.

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Question re: extracting functional data from cortical ROIs
by Dan Dillon 20 Mar '08

20 Mar '08

I have a question about extracting functional data from structurally defined cortical labels. Here's what I'm doing: 1) Run a gammafit analysis; 2) Define cortical ROIs by using mri_annotation2label to make labels from aparc.annot; 3) Define sub-cortical ROIs by using mri_cor2label to make labels from aseg.mgz; 4) Extract functional data from labels using func2roi-sess; 5) Summarize the data with roisummary-sess. I usually view the cortical ROIs on the inflated (or pial) surface and the subcortical ROIs in the volume, and they usually look great. But when I view the cortical labels in the volume, they seem to consist of a 1-voxel thick strip hugging the white matter; they don't seem to cover the gray matter at all. Does this mean that I am extracting functional data from a 1-voxel thick strip (!), or am I just mis-understanding something about how a cortical label appears in the volume? Also, I know that "white" is the default surface in mri_annotation2label, but if I switch to "pial", make a label, and view it in the volume, it still looks like a 1-voxel thick strip, just around the outside edge of the gray matter (instead of around the inside edge if I use "white" as the surface). My simple mind wonders why these cortical labels-which look great on the inflated brain-don't cover the region between the pial and white surfaces (i.e., the gray matter) in the volume. Am I making a basic error here? If so, what do I need to do to extract functional data from cortically-defined ROIs? I am running version 4.0.2. Thanks! Dan D.

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Question about functional analysis
by lan lin 19 Mar '08

19 Mar '08

When we use freesurfer to do functional analysis(such as PET), do we need to account for global mean? thanks

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Question about slopes
by Jerry Yeou-Wei Chen 19 Mar '08

19 Mar '08

Hello, The attached image shows a plot generated from a design with one continuous variable (gender) and three continuous variables (called N, E, P), analyzed using the "old" method via command line rather than QDEC. For mri_glmfit, the DODS option was used and the contrast was 0 0 1 -1 0 0 0 0 (to compare the relation between N and thickness, in females versus males). I am wondering why the fitted lines seem to be so far "off" from the actual data points. Could anyone please shed some light on this issue? Please let me know if you need any more information about our analysis. Thanks, - Jerry

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mri_glmfit...
by Cameron Ellis 19 Mar '08

19 Mar '08

Hi all, Does mri_glmfit run to correlate volume with a particular measure identify clusters on a voxel by voxel basis or does it compare the aseg volumes of the different subcortical structures? Thanks, Cameron

2 1

QDEC limited regressors
by Jerry Yeou-Wei Chen 19 Mar '08

19 Mar '08

Hello, I would like to know why we are limited to 4 regressors in the design specification within the QDEC GUI. If I understand correctly, there is no such limitation in the "old" method (via command line). Thanks, - Jerry

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