Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

tkmedit-sess question
by Avram Holmes 05 Jun '07

05 Jun '07

FreeSurfer Folks, I am attempting to look at some data with tkmedit-sess tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold but I am getting the following error. corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info Error: Loading volume orig Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work? Thanks, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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how to import private color scales
by Istvan Akos Morocz 04 Jun '07

04 Jun '07

dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

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problem with tksurfer (fwd)
by Claus Tempelmann 04 Jun '07

04 Jun '07

Hello everybody, Having worked with quite old versions of freesurfer for a long time we decided recently to install a newer version on two new computers. Both are running under the 64 bit version of SUSE Linux 10.2, both have a Dual Opteron processor, they have 6 GB (system 1) or 8 GB (system 2) and most hardware and software is quite comparable in my opinion. There is one major difference with the graphic cards, system 1 has an MSI GEForce 6600, whereas system 2 has an GEForce FX 7600GS. I'd expect that both cards are more than sufficient for freesurfer and I doubt that this difference can be the reason for the difference I have observed but may be some of you have experienced a similar problem and can help me out. What's the problem? All analysis steps of the standard procedure seem to work fine on both systems. However, I see a reproducible strange problem on system 2 when I try to use tksurfer on the standard data set (bert) coming with the package (freesurfer-Linux-rh9-stable- pub-v3.0.5.-full.tar). When I run the command tkregister bert lh inflated on system 1, everything looks like expected. But on system 2 something is wrong, the program tells the number of vertices and faces as usual and the numbers are the same as on system 2 (as they should, I'm using the same data set). Nevertheless, the output looks quite different, I'll try to attach a screenshot. The window shows up as usual and a small part of the inflated brain is shown at the right edge of the window but the rest of the brain is never shown. When I rotate this surface the visible part of the inflated brain is rotated correctly but the rest is always missing. Can anybody help? Thanks in advance Claus ----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany

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Masking at the individual level
by Dan Dillon 04 Jun '07

04 Jun '07

Dear FreeSurfers, Quick question about masking. I routinely make a brainmask for each subject and include the mask flag in the mkanalysis (see below), but I note that when I run contrasts and plot results-either for individual subjects or for group-level stuff-I get statistical results for voxels outside the brain. I'd like to mask the extra-brain voxels out at the individual level, so that they don't get included at any point in my group level analyses. How do I do this? More generally, does the brainmask serve only a visual/display function or can I use it to constrain what I'm doing stats on (which is what I want it to do)? Thanks for your endless help! Dan Dillon PS. This is a a typical mkanalysis step . . . mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm mg_3_7.par -designtype event-related -funcstem fmcs tcsm6 -nconditions 13 -polyfit 2 -taumax 30 -inorm -mask brain -timeoffset -1.25 -TER .1 -autostimdur -force

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ANCOVA model in Freesurfer
by Juergen Haenggi 04 Jun '07

04 Jun '07

Dear Freesurfer users I am trying to create the GroupDescriptorFile 1 for an ANCOVA in order to analyze local cortical thickness. I intend to compare two groups while controlling for age and mean cortical thickness. Am I right that I can leave out the term "class" and model group as a variable? GroupDescriptorFile 1 Title CorticalThickness Variables Group Age MeanThickness Input Control01 ControlSubject 27 3.14 Input Control02 ControlSubject 31 3.28 .... Does the variables all have to be integers or can it be also a string? Thanks for helping Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Situation with OASIS
by Martin Kavec 04 Jun '07

04 Jun '07

Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results of your great effort available? Thanks in advance for the great job (and reply of course). Martin

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color coding for parcellations/regions of interest
by Lars M. Rimol 03 Jun '07

03 Jun '07

Hi, I have combined the Desikan parcellations into regions of interest, which I would like to visualize. So I need to create an ad hoc color coding scheme. In order to visualize the ROIs I would load a file equivalent to the ?h.aparca2005s.annot file, which would show the same color for those parcellations that belong to one and the same ROI. Which file contains those color definitions, or in other words which file do I need to modify in order to be able do that? Tank you! -- yours, LMR

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tkmedit scripting
by Sebastian Moeller 02 Jun '07

02 Jun '07

Hi List, getting into scripting of freesurfer I wonder whether it is possible to script false discovery rate for overlays in tkmedit. There seems to be Overlay_SetThresholdUsingFDR, but it is not really documented. So, here my question: what is the invocation to use FDR to select the thresholds for overlay 1, without any masking? thanks & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_vol2surf question
by Morgan Hough 01 Jun '07

01 Jun '07

Hi there, I am trying to interpolate a volume of tstats to the average surface with mri_vol2surf but I am getting the error below. Does mri_vol2surf take all the inputs that mri_convert takes? Is this a float2int problem mentioned in the bugs section of the --help? If the latter, what argument should I specify with --float2int? Thanks in advance for your time. Cheers, -Morgan mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.vbm_surf_results.mgh --srcreg reg.dat srcvol = vbm_results_mni305_tl.nii.gz srcreg = reg.dat srcregold = 0 srcwarp unspecified surf = inflated hemi = lh trgsubject = average surfreg = lh.sphere.reg interp = nearest float2int = round INFO: float2int code = 2 niiRead(): error opening file /home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24

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spm_hrf mkanalysis-sess question
by Avram Holmes 01 Jun '07

01 Jun '07

All, I am interested in comparing a gamma fit analysis with the spm_hrf method. Unfortunately I am unable to use the '-autostimdur' or the '-TER' flags in with the SPM mode. When I do use these flags I get the following error... 'ERROR: paradigm is ill-conditioned (6.06514e+13). Check your paradigm file for file for periodicity's or for some event types that all ways follow other event types (or itself). Saving Xfinal to /Raid/shared/exp/CONCON/fMRI/functional/c01/Flanker/Flanker_SPM2/h0.sumxtx.mat It could also be due to the fact that the TER does not equal the TR. SubTR estimation only works when the event schedule has been optimized with SubTR estimation in mind.' Thanks for your time, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Freesurfer June 2007