Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

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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Subcortical Label
by Kelly Silva 08 Jan '09

08 Jan '09

Hello, I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_vol2surf - MNI subject
by Yigal Agam 08 Jan '09

08 Jan '09

Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal

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Trouble Creating label
by Zeidan, Mohamed A. 07 Jan '09

07 Jan '09

Hello all, I'm creating a label on a volume in tkmedit and as I do it, tkmedit will unexpectedly close and give me the following error message in the terminal window: =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... Any thoughts? Thanks, Moe

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Freesurfer January 2009