Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Catching uncorrected results sig.mgh
by Antonella Kis 23 Feb '12

23 Feb '12

Dear All, I would like to know what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one. Many thanks. AK

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ICV
by Dusan Hirjak 23 Feb '12

23 Feb '12

Dear Freesurfer experts, I am a beginner in using Freesurfer. I was wondering if ICV should be treated as a potential confounder (such as age, education, chlorpromazine equivalents and duration of illness) in the statistical analysis of volumetric data/cortical thickness? Thanks in advance! Dusan

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problems with dti data in magnetom skyra 3T
by John Fredy 22 Feb '12

22 Feb '12

Hello all, I am trying to use a set of dti data from a Magnetom Skyra 3T. I use the dt_recon process with data from another siemens of 1.5T without problems. With the Skyra 3T I have the following error in the log file: MRIresample(): error inverting matrix; determinant is nan, matrix is: Can someone help me with this problem? Thanks in advance John Ochoa Universidad de Antioquia

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Vertex size and vertex value export
by Dalwani, Manish 22 Feb '12

22 Feb '12

Hello Freesurfer's, What is the size of a vertex? Also, how do you define a vertex? Also, in the Qdec analyses, once you get a cluster and the maximum vertex, is there a way to export individual vertex value (for each subject)? Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado

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Cluster position
by Antonella Kis 22 Feb '12

22 Feb '12

Dear All, Is there a way that I can get my clusters location (segmentation and/or annotation) inthe MNI space if I know the MNI coordinates? Many thanks. AK

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memory and bus failure
by cloud.ctrl＠me.com 22 Feb '12

22 Feb '12

I have three scans that exit with errors that I cannot comprehend. The first two indicate memory and bus failures, so I thought maybe my computer had choked during processing, but after running again I received the same errors. The third is too cryptic for me to understand at all. Can anyone offer any advice for these? 1: BEST FITNESS (o)is 321.33384 mri =0.000 curv = 2.540 unmri = -331.493 ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) mris_topo_fixer(58671) malloc: *** mmap(size=534511616) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRISalloc(1142113, 468): could not allocate vertices Cannot allocate memory 2: searching scale 1 Z rot 65.8 searching scale 1 Z rot 66.1 searching scale 1 Z rot 66.3 global minimum found at slice 126.0, rotations (22.40, 59.33) final transformation (x=126.0, yr=22.402, zr=59.329): 0.472 -0.860 0.194 140.992; 0.795 0.510 0.328 -83.378; -0.381 -0.000 0.925 33.641; 0.000 0.000 0.000 1.000; Bus error 3: CORRECTING DEFECT 37 (vertices=32782, convex hull=6402) normal vector of length zero at vertex 95333 with 0 faces vertex 95333 has 0 face No such file or directory

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Trac-all -preproc cannot find cor-.info
by Martijn Steenwijk 22 Feb '12

22 Feb '12

Dear all, I'm trying to run trac-all (FS5.1, the updated trac-all) for a provided nii.gz DWI volume and it's bvals/bvecs. During the preprocessing mri_convert searches for dti/COR-.info, but cannot find it - see log below. Does anyone have a clue why it searches for this COR-.info file? Best, Martijn #------------------------------------- /usr/local/freesurfer51/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Feb 22 13:45:42 CET 2012 mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/raw.nii.gz... TR=13000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.994366, -0.0972332, -0.0422076) j_ras = (-0.0971699, 0.995259, -0.00408943) k_ras = (-0.0424052, -3.49181e-05, 0.999101) writing to /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz... cp /haso/msteenwj/test_data/V3T/dti/bvecs_old /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs cp /haso/msteenwj/test_data/V3T/dti/bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals flip4fsl /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -2.39997 fslswapdim /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz x y z /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvecs /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvecs mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvals mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz corRead(): can't open file /haso/msteenwj/test_data/V3T/dti/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/... Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 22 13:52:47 CET 2012

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Freesurfer and MATLAB
by Antonella Kis 22 Feb '12

22 Feb '12

Dear All, Is there a way that I can open my rh.aparc.stats files (saved in stats after recon-all) in MATLAB as a matrix? I would like to concatenate all the rh.aparc.stats files from all my subjects. Many thanks, Antonella

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Nearst Cortical Label (Annotation) for the CVS space
by Antonella Kis 22 Feb '12

22 Feb '12

Dear Doug, I wonder if you could get the chance to finish the work regarding the Nearest Cortical Label (Annotation) for the CVS space. Also, I have few questions and I will appreciate if anyone can help: 1) Can I get more clusters after I correct for multiple comparison than the number of clusters I have in the uncorrected results? Is this possible? 2)When I change the smoothing from fwhm 10 to fwhm 20 for example why I am loosing from my clusters (uncorrected results)? Also in this case my clusters show became larger no? 3) I found my significant clusters after multiple comparisons for the FA group analysis study and I would like to dilate all regions for a better visualization, using the dilM function of the FSL tool fslmaths.Can you please advise me how to do it if I have the significant clusters file permcsd.sig.cluster.mgh? 4) As I mentioned before,I completed my DTI group analysis at subcortical level on the CVS space and found clusters that survived by multiple comparisons. The results shows that FA is decreasing in patients vs. controls. I used then the same subjects to do a structural group analysis to compare the cortical thickness between the two classes. I found some clusters on the fsaverage but this time they different located then the clusters found in my DTI data. Is this right? I suppose it should be since I compare two different data sets for the same subjects: FA clusters on subcortical CVS space vs. structural data on the fsaverage. I still found that my cortical thickness is decreasing in patients vs. controls but is there any relation that I can established between the two studies? Can I merge my structural results with my subcortical results? I was reading about this on your webpage:http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastG… but I am not sure if in this case the structural analysis is using the same functional data set while in my case I have same subjects but structural data for the structural group analysis and DTI data for the subcortical analysis. Can you please make this a little clear for me? How can I run a structural analysis on my DTI data? Many thanks!Antonella

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tksurfer error
by Signe Bray 22 Feb '12

22 Feb '12

Hi, I have been experiencing an error with tksurfer. It occurs when I am trying to generate an occipital patch, following these instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I open a surface using: tksurfer <SUBJ> lh inflated -curv lh.curv Following the steps, when I click the surface and press the "Fill Uncut Area" button, tksurfer crashes with the following error: tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. I have also experienced this problem zooming out on a specific surface patch. I have seen this problem in different forms on the mailing list, but have not seen any solutions or workarounds: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19846.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.htmlhtt… My machine info: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-8-generic x86_64 --------------------------------------------------------------------- Thank you, Signe

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Freesurfer February 2012