Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

fixing segmentation errors
by Jared Price 10 Jan '09

10 Jan '09

Hello freesurfers! We have a large data set which has segmentation volumes that have been manually labeled. Along the way occasionally a voxel which should have been labeled as left-hemisphere was labeled with the corresponding right-hemisphere label. For example, there might be a few voxels in the right putamen labeled as left putamen. Is there a quick fix for this? Thanks, Jared

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how is a path created?
by Michael Harms 09 Jan '09

09 Jan '09

Hello, I was wondering what approach is used to connect marked vertices when using the "Make Path" and "Make Closed Path" tools of tksurfer. Does the "connecting" operation just use the shortest (geodesic) distance between vertices, as determined by the currently displayed surface? Does the 'mri_path2label' binary use the same algorithm? And, is there any mechanism for taking curvature or sulcal depth into account? (e.g., connect points along a line of minimum or maximum curvature change, rather than using geodesic distance) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_surfcluster problem?
by Lauren LaCount 09 Jan '09

09 Jan '09

Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like: mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01 (in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x) When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000. Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere? Thank you! -Lauren -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lauren LaCount Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149, 13th St. Charlestown, MA 02129 llacount(a)nmr.mgh.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Freesurfer] Can freesurfer flatten (and dsiplay) certain subcortical areas?
by Koen Van Leemput 09 Jan '09

09 Jan '09

We have recently developed a method for automatically segmenting the hippocampal subfields from ultra-high resolution MRI data. The software code is not yet in FreeSurfer, but will be in the future. It produces volumetric segmentations, rather than surface representations, though. - Koen > > Can freesurfer flatten (and only display) a (or several) segmented > subcortical area(s), e.g. hippocampal region? If yes, can the fine > structures in such a region (such as CA1,2,3, DG, etc.) be labeled? > > > > Thanks, > > Mingwu

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To ask you about mismatch in TR in FSFAST low level analysis
by Francisco Robles 09 Jan '09

09 Jan '09

Hi Freesurfer users, My Name is Francisco Robles, from México City, and I am writing you to ask you a doubt about the selxavg3-sess process with FS-FAST. The error is the following: it seems like the TR from the analysis is 1.75 (specified in mkanalysis gui) and from data (but i dont know in waht file) is 1750 (like it is in milisecs), does anyone knows how can i edit the TR from data to put it similar with the TR from analysis?. Thak you very much... the incomplete process is the following: LINGUISTICA:/usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1> selxavg3-sess -s 001 -analysis m1-gamma-fwhm6 -overwrite -------------------------------------------------------------- selxavg3-sess logfile is /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/log/selxavg3-sess-bold-m1-gamma-fwhm6-090109121039.log -------------------------------------------------------------- ------------------------------------------- /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001 vie ene 9 12:10:39 CST 2009 anadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 analysis m1-gamma-fwhm6 alread exists for 001 ... reanalyzing (deleting old analysis) ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.336 (R2007a) January 29, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1 Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 in-v-irr.mat 2 in-v-reg.mat 3 ini-v-0.mat 4 inr-v-0.mat 5 inr-v-ini.mat 6 pa-v-pr.mat 7 pai-v-0.mat 8 par-v-0.mat 9 par-v-pai.mat 10 pri-v-0.mat 11 prr-v-0.mat 12 prr-v-pri.mat 13 reg-v-irr.mat Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. nruns = 1 autostimdur = 1 outanadir = /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/m1-gamma-fwhm6 Found 39377/122880 (32.0) voxels in mask Creating Design Matrix Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ntptot = 239, nX = 15, DOF = 224 XCond = 132.651 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.508299 (t=0.061196) 2 -0.25 -0.274155 (t=0.125188) 3 0 -0.0471794 (t=0.195066) 4 0.25 0.168481 (t=0.239998) 5 0.5 0.361722 (t=0.311806) AR1 Correction M: 0.0685 1.14384 Computing contrast matrices Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 1 in-v-irr J= 1 eff = 3.3 vrf = 3.3163 vrfffx = 3.3163 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 2 in-v-reg J= 1 eff = 3.6 vrf = 3.5874 vrfffx = 3.5874 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 3 ini-v-0 J= 1 eff = 11.1 vrf = 11.0570 vrfffx = 11.0570 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 4 inr-v-0 J= 1 eff = 7.3 vrf = 7.3329 vrfffx = 7.3329 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 5 inr-v-ini J= 1 eff = 5.6 vrf = 5.5884 vrfffx = 5.5884 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 6 pa-v-pr J= 1 eff = 4.3 vrf = 4.2514 vrfffx = 4.2514 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 7 pai-v-0 J= 1 eff = 10.1 vrf = 10.1026 vrfffx = 10.1026 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 8 par-v-0 J= 1 eff = 16.5 vrf = 16.5397 vrfffx = 16.5397 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 9 par-v-pai J= 1 eff = 7.1 vrf = 7.1292 vrfffx = 7.1292 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 10 pri-v-0 J= 1 eff = 16.4 vrf = 16.4187 vrfffx = 16.4187 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 11 prr-v-0 J= 1 eff = 10.4 vrf = 10.3983 vrfffx = 10.3983 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 12 prr-v-pri J= 1 eff = 7.4 vrf = 7.4063 vrfffx = 7.4063 r = 1.00 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. 13 reg-v-irr J= 1 eff = 3.3 vrf = 3.3480 vrfffx = 3.3480 r = 1.00 OLS Beta Pass run 1 t= 0.1 Loaded /usr/local/freesurfer/subjects/neurolinguistica_subjs/ROBLES/FS-data/Functional/fr1/001/bold/001/morfo1.par as a par4 file. ERROR: TR mismatch between analysis and data analysis TR = 1.75, data TR = 1750 >> ------------------------------------------ ERROR: fast_selxavg3() failed\n _________________________________________________________________ Windows Live mantiene tu vida digital en sincronía. http://download.live.com

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Single subject statistical analysis
by Jürgen Hänggi 09 Jan '09

09 Jan '09

Dear FS statistical experts We would like to compared a single subject against a group using FS statistical machinery. There is a paper by Salat et al., Hippocampus, 2006, in which the amnestic patient H.M. was compared against 4 control subjects. How valid is such a statistical test in FS? Does the variance (incl. error variance) is estimated across both groups (pooled variance)? Thanks for help Regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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Can freesurfer flatten (and dsiplay) certain subcortical areas?
by Mingwu Jin 08 Jan '09

08 Jan '09

Can freesurfer flatten (and only display) a (or several) segmented subcortical area(s), e.g. hippocampal region? If yes, can the fine structures in such a region (such as CA1,2,3, DG, etc.) be labeled? Thanks, Mingwu

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Top Quartile of Active Voxels
by Dave Brohawn 08 Jan '09

08 Jan '09

Hello, I ran the following analysis to target task-specific voxels at a certain contrast and offset. func2roi-sess -roidef dACC10_lh -analysis EMerror -anatlabel dACC-lh -maskcontrast ASevfix -maskframe 5 -maskthresh 1 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR I would like to create a functional constraint including only the 25% most active voxels (top quartile). Is there a command that can achieve this? Thanks, Dave Brohawn

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Problem running tksurfer
by Yigal Agam 08 Jan '09

08 Jan '09

tksurfer fsaverage lh inflated surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/schnook_001/users/yigal/projects/functional surfer: Reading header info from /autofs/space/ventzl_001/users/SUBJECTS_DIR/fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 Loading /usr/local/freesurfer/stable4/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable4/lib/tcl/tkUtils.tcl Error loading icon_disk_multiview: couldn't open "/usr/local/freesurfer/stable4/lib/images/icon_disk_multiview.gif": no such file or directory Error sourcing /usr/local/freesurfer/stable4/lib/tcl/tksurfer.tcl: image "icon_disk_multiview" doesn't exist reading white matter vertex locations...

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File cnr.mgh
by Jürgen Hänggi 08 Jan '09

08 Jan '09

Dear FS experts I am not sure whether the file cnr.mgh represents the contrast-to-noise ration (CNR) on one hand and how to interpret it. When I loaded the cnr.mgh in tkmedit, there is actually no image visible and only one value is shown e.g., 0.355 or -0.965. What do these values mean? In my opinion, these values are to small for a classical CNR, isn't it? Can I use the cnr.mgh file to control the CNR (and also the SNR) of the FS surfaces derived from images acquired on two different scanners? Is there another way in FS to check whether the SNR and CNR is comparable between surfaces derived from images acquired on different scanners? Thanks in advance Kindly regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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