Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

topology fix error
by Cameron Ellis 17 Jan '07

17 Jan '07

Hi all, I received the following error while running autorecon. Has anyone come across this before who knows what to do to fix it? Cameron Command run: recon-all -subjid SM1S17_autoreconall -autorecon2 Error Script: #@# Fix Topology lh Wed Jan 17 04:00:20 EST 2007 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm /autofs/space/troy_003/users/retrievalnewest/SM1S17_autoreconall/scripts mris_topo_fixer -mgz -warnings SM1S17_autoreconall lh verbose mode on (medium mode): printing warnings Before topology correction, eno=-64 (nv=132420, nf=264968, ne=397452, g=33) Surface Diagnostics: eno=-64 (nv=132420, nf=264968, ne=397452) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold The original surface does not self-intersect The surface has 33 loops (X=-64) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 5383 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) INFO: assuming .mgz format reading input surface /autofs/space/troy_003/users/retrievalnewest/SM1S17_autoreconall/surf/lh.orig... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (77.69) < WM (97.20) ] Computing Initial Surface Statistics -face loglikelihood: -6.3839 (-3.1919) -vertex loglikelihood: -6.2470 (-3.1235) -normal dot loglikelihood: -3.6517 (-3.6517) -quad curv loglikelihood: -5.7654 (-2.8827) Total Loglikelihood : -22.0480 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number 3 (-1 loops) computing statistics for defect 1: 55 vertices location: [ (135,115,184) - average intensity = 81.597 ] -gray ( 77.69 , 5.73 ) -white ( 98.05 , 2.73 ) -gray ( 80.21 , 20.72 ) -white ( 98.85 , 18.30 ) -intensity (77.686409 [log = -2.909158 ]- 98.046989 [log = -1.932804 ]) -curv (k1=-0.161 (0.638) , r1 = 6.211 | k2=-0.049 (0.152), r2 = 20.453 ) -curv (k1=-0.130 (0.684) , r1 = 7.700 | k2=-0.023 (0.257), r2 = 43.903 ) MRISalloc(-155, 424): could not allocate vertices Cannot allocate memory Linux node0344 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jan 17 04:01:31 EST 2007

2 1

Label folder
by Juergen Haenggi 17 Jan '07

17 Jan '07

Dear Freesurfer users we are running Freesurfer 3.0.4. (64bit) on a grid computer. If we run recon-all -all with the -dontrun flag, everything is fine. But if we then run the analysis, it run until it tried to write the /label/lh.aparc.annot file. The Freesurfer said there is no directory called "label". But this directory was there and I guess that Freesurfer itself has deleted the label directory. Does anyone had a similar problem or any idea where the problem is? Thanks a lot in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

2 1

mesial temporal lobe gyrus
by tulu 16 Jan '07

16 Jan '07

Dear freesurfer experts, I use the latest version of freesurfer 3.0.4 to study pial thickness. I found the part of mesial temporal lobe did not included in pial surface in many cases(see figure). Is it correct ? should I add the control point to every cases ? Thanks replay Kl chen

2 1

segmentation fault
by Cameron Ellis 16 Jan '07

16 Jan '07

Hi, I attached a text file of the reconall log for a subject which lists a segmentation fault that I have received. I have corrected the talairach transform for this subject, checked the inorm and skull strip and continue to receive this error. There are some minor bumps on the inflated surface that correspond to some locations in the wm.mgz where the wm extends very slightly beyond the pial surface. How can I tell if this is leading to the segmentation fault and if it is worth correcting? Can I tell from the error message or do i just have to correct this and rerun recon2 and 3? I also included a tiff of lh.inflated and one of a defect in the wm.mgz that can be seen on the surface. Any advice is greatly appreciated! Thanks, Cameron

2 1

matlab load/save mgh
by Jed Jeng 16 Jan '07

16 Jan '07

Hi, I've been using the matlab scripts to load and save mgh files. I've noticed a difference in the precision in my original volumes and the ones I've saved with matlab. Namely, after saving a volume with matlab and loading it up in tkmedit I notice that everything now has an extra 2 digits of precision (aka. voxels with an intensity of 100 now have an intensity of 100.00). Is there any way to remedy this small problem? I've used an integer array in matlab, and I've tried to just mri_convert the volume in hopes that it would truncate the values. I'm only asking because cor2label won't work with the matlab saved volumes. Any help is appreciated. Thanks! ~Jed

2 1

VNC/GLX... what is really vncserver.glx
by Yaroslav Halchenko 16 Jan '07

16 Jan '07

Dear Freesurfer People, >From http://surfer.nmr.mgh.harvard.edu/fswiki/RemoteAccess we found out that it seems MGH people have some custom script or a VNC server (named vncserver.glx) which GLX support good enough to run freesurfer within VNC session. We have been using standard vnc4server which provides GLX capabilities but unfortunately seems not all, so whenever we run tksurfer (for instance) we get a lengthy list of following errors and opengl canvas not painted at all ,------------------------------------------- | Received X error! | Error code : 158 | Request code : 148 | Minor code : 2 | | Error text : 'GLXBadLargeRequest' `--- Could you please advice on what VNC server solution you are using for freesurfer -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

2 2

convert xfm to dat?
by Benjamin Simon Thompson 16 Jan '07

16 Jan '07

Hello I am using fsfast to perform a retinotopy analysis. The initial stages are working well, however when I come to register my low-resolution functional scans to my high-resolution anatomical data using spmregister-sess I get a poor regestration which is very time-consuming to correct with tkregister-sess. From a separate analysis on this data using MINC tools I have a .xfm regestration file that registers my low resolution data (in .mnc format) to my high resolution data (also in .mnc format). Is there any way I can convert this xfm file to the .dat file required by FSFAST? Thanks, Ben

1 0

I have one question!
by zhang yi 15 Jan '07

15 Jan '07

Hi, When I was using freesurfer I met one problem: After I installed freesurfer, I entered the command "tkmedit bert orig.mgz" to see whether it does work, but the ubuntu windows closed and then restart again to the login in window. So, I do not know what's wrong with it? Can you help me to deal with the problem? I am appreciate your help! zhang yi zhang yi 2007-01-15

2 1

problem about ubuntu
by chin wei 15 Jan '07

15 Jan '07

hi all. I installed freesurfer in an ubuntu linux. But when I perform the test code "tkmedit bert orig.mgz", the system was logged off. Could somebody help me? Thanks you in advance.

2 1

lesions
by Joan Fisher 14 Jan '07

14 Jan '07

Lots of questions about lesions: 1) What is the best way to measure the size of a lesion in Freesurfer? Or should it be drawn in afni and transported to Freesurfer somehow? 2) What is the best way to measure how much of each ROI is affected by the lesion? 3) Line 25 lists "Left-lesion" and Line 57 lists "Right-lesion" in aseg.stats, but these are currently all zeros in brains that have clear lesions -- why? And why are those lines there if Freesurfer isn't recognizing a hole in the head as a lesion? Is there some option that must be selected to make this work? 4) Is it true that cortical lesions can throw off Freesurfer's ability to see landmarks, so that not only the lesion area might be mislabeled, but surrounding tissue and even distant tissue too? If so, is there a way around this problem built into Freesurfer? I have one brain with a large cortical lesion that looks like it parcellated okay, and another with a huge lesion that doesn't look right at all. Periventricular lesions look fine -- is this what others have found? 5) What is the best way to dump the parcellation data and the subcortical segmentation data back into afni (which files specifically) so that it can be viewed in 3D on the original structural brain as a mask? Help would be much appreciated. Many thanks, Joan Fisher University of Chicago

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