Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

single set of DICOMS
by Catherine Alexandra Hartley 21 Jan '07

21 Jan '07

Hi, I'm just beginning to use FreeSurfer and I have a very basic question. I'm doing a reanalysis of an existing data set looking at behavioral correlates of cortical thickness in a particular ROI. I only have one set of DICOMS for each subject. Is it ok to do the analysis on a single set of structural data or would the level of inaccuracies resulting from not averaging across multiple scans be undesirable? Thanks, Cate

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RE: [Freesurfer] control points and white matter edits
by Tanji, Kazuyo (NIH/NIMH) [F] 18 Jan '07

18 Jan '07

Dear List, I have a similar problem with getting accurate pial and white matter surfaces in monkey inferior temporal, frontal and occipital regions. In those areas surfaces are not recognized properly. I tried putting control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was mentioned somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate it if you could suggest any other ways to correct this problem. Thanks, Kazu > Hi Paul, > > The inferior temporal regions are the trickiest, especially in low > quality scans - without seeing any images, you may have achieved as > close as you are going to get. > > Be careful with control points, more is not always better, quality > over quantity, you want to be sure you have put them in correct > locations, not on partial volumed voxels, and only in regions that are supposed to be wm. > > While adding voxels to the wm volume will have some impact on where > the final surface lays, it is also dependant on finding the best > intensity gradient. If your scans are lower quality with intensity > troubles that will likely trump any edits you've made. > > If you'd like to upload one of your subjects I am happy to take a look > at it > - although I will be out of town all next week so it might take me a > while to get to it. > > Jenni > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg > Sent: Friday, January 05, 2007 7:04 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] control points and white matter edits > > Hi all, > > I'm having trouble getting accurate white and pial surfaces in > inferior temporal regions on a few lower quality scans with > significant intensity variation. I've added hundreds of control > points and drawn in white matter in these regions when control points > failed to recover unlabeled cortex, but when re-running the scripts > with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 > the surfaces are still not accurate. Are there other interventions I > can to to get more accurate surfaces? If you manually add white > matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? > > Thanks, > Paul

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buckner data set
by joel-bruss＠uiowa.edu 18 Jan '07

18 Jan '07

Just a quick question. Is the vitamin E capsule (or whatever the bright artifact outside the skull/skin is) denoting the right or left hemisphere for the Buckner 40-brain data (look at subject buckner_data/group_study/004/mri/rawavg.mgz)? Thanks, Joel

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disabling hypointensities
by Dominick, Kelli, Ray Carpenter 18 Jan '07

18 Jan '07

Hi, I would like to disable the labeling of hypointensities. Is there a command I can use in order to do that? Thanks! Kelli

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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

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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) ----------------------------------------------

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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

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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

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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

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