Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30087 discussions

contrast matrix for 2 discrete factors and 3 continuous variables
by Jose Luis Cantero Lorente 18 Jan '11

18 Jan '11

-  Dear Freesurfers, My experimental design includes 2 discrete factors and 3 continuous variables: Discrete factors: - Diagnosis with three levels (A, B, C) - Gender with two levels (Males, Females) Continuous variables: - Mean cortical thickness in the left hemisphere (CTLH) - Age - Performance in a memory test (TASK) The FSGD file would be as follows: GroupDescriptorFile 1 Title Thickness-subj Class AMale Class AFemale Class BMale Class BFemale Class CMale Class CFemale variables ZCTLH ZAGE Input control_01 AMale -1.04398 0.24789 Input control_02 AMale 1.22853 -0.72343 Input control_03 AFemale .13773 -1.37097 Input control_04 AFemale .41043 0.24789 Input mci_01 BMale -.77128 0.24789 Input mci_02 BMale -2.40749 0.73354 Input mci_03 BFemale -.86218 -1.0472 Input mci_04 BFemale .50133 0.23777 Input ad_01 CMale -.75678 0.22789 Input ad_02 CMale -2.88749 0.63047 Input ad_03 CFemale -.96015 -1.4452 Input ad_04 CFemale .80712 -0.37567 … We are assuming different offsets and different slopes (DDOS). The following contrast would test the null hypothesis whether there is a difference between B and C (T-test) regressing out the effect of the remaining variables. 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Could you help me to build the contrast for testing interactions in the above experimental design? In the FSwiki examples, you add one column when you have two factors with two levels each, and one continuous variable. I am not sure how many columns should I add in our particular case and why. Null hypothesis: is there an interaction between diagnosis (B > C) and gender regressing out the two remaining variables? Assuming that you add one column per variable that is regressed out, the contrast would be as follows: 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Is this correct? Any help will be very appreciated. Many thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Converting nii to label....
by Joseph Andreano 18 Jan '11

18 Jan '11

Hi, I have a volume in .nii format which I would like to use as an ROI to extract signal from, using func2roi-sess. However, func2roi requires a label. How would I convert a .nii volume to a label? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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mkanalysis-sess -gui
by Iris.steinmann 18 Jan '11

18 Jan '11

Hi Freesurfers, I have a little problem: I use a linux mashine with ubuntu 10.10 and installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz.. Most commands are working well (like tkmedit, tksurfer …), but I have a problem to get an analyse gui with (mkanalysis-sess -gui). I just get a long error report from matlab. I created a startup.m file for matlab like the following: %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% addpath('~/freesurfer/matlab/'); Does anyone has an idea what could be wrong? I would be so thankfull! Iris

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two issues with the processing stream
by Ilana Hairston 17 Jan '11

17 Jan '11

Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted. thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** What might have been is an abstraction Remaining a perpetual possibility Only in a world of speculation T.S. Eliot

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How to make a surface overlay?
by Ed Gronenschild 17 Jan '11

17 Jan '11

Hi, I've done some statistics on thickness and volume of the default cortical regions (segIDs 1000 - 1035 and 2000 - 2035) for a number of subjects. How can I show for instance the p values (expressed as -log(p)) as an overlay on the pial surface of fsaverage? Ed

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brain volumes from different freesurfer versions
by qtnguyen＠nmr.mgh.harvard.edu 16 Jan '11

16 Jan '11

Dear freesurfers, We are trying to find a reliable measure of the total brain volume and have been finding it difficult to get a consistent measure across our subjects since they were reconstructed using different versions of freesurfer. Some of our subjects were reconstructed using version v 1.69.2.1 while others used v 1.33 After searching through the mail archive, we decided to use the following command (mri_segstats --seg aseg.mgz --brain-vol-from-seg --sum segVOL) We are thinking of using the "Brain Segmentation Volume Without Ventricles" from the output file as our total brain volume in our analysis. Will this value be constitent and reliable across the reconstructions using different versions of freesurfer? Thank you in advance! Trang

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rerun the previous editted Freesurfer result
by Jin Li 15 Jan '11

15 Jan '11

Hi, Freesurfers. Last time I used Freesurfer v4.5 first, manually corrected the data, then ran the rest steps in Freesurfer v5.0. As Bruce suggested, I should rerun the data. Actually the visual check and manual correction steps have taken me one month as we have hundreds of data, so I really hope to use the previous edits. If I hope to get the v5.0 outputs, can I rerun the data with previously corrected edits? In another word, if I previously sub001 was only editted on its pial surface.In this rerun process, can I run the first stages including pial surface generation (stages 1-21), then replaced with the previously edited pial surface, then run the rest stages(21-31)? Is this acceptable, or is there any other ways to rerun the data and can take use of previous edits? Thank you very much for all your suggestions. Jin

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Re: [Freesurfer] tksurfer display problem
by Alexander Lebedev 15 Jan '11

15 Jan '11

Hello, Mr. Watson, I had the same problem with ATI videocard on 64-bit CentOS 5.5. It was solved after installation of last "Catalyst" driver (After disabling SELinux: http://www.crypt.gen.nz/selinux/disable_selinux.html.) - ***I am not quite sure which driver you should use with nvidia. I would also advice to check for errors your installation "log"-file (It must located in your n-vidia directory somewhere inside /usr/share/). For example, my problem was connected with GCC (I noticed errors inside log file and installed all necessary libraries). Hope it helps. -- Best Regards, Alexander Lebedev I.P. Pavlov State Medical University 197022, Lev Tolstoy str. 6/8 Saint Petersburg, Russian Federation tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: alexander.vl.lebedev

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Measuring the cortical thickness
by Siti Hajar 15 Jan '11

15 Jan '11

I want to measure the cortical thickness of my ROI. When i ran, mri_segstats --seg fsavegagepath/hemi.fsaverage.hemi_roi_subj.mgh --in hemi.thickness.fsaverage.mgh --sum segstats-hemi_roi_subj.txt -----> in order to find the --sum segstats, error occured: Error:dimension mismatch between input volume and seg input 16342 1 1 seg 23406 1 7 but when i tried again using the old version of freesurfer, freesurfer_Linux_centos 4_x86_V4.4, it worked... "0 0 163838 163838 1 1 4 4 reporting on 2 segmentation." Can you helping me explaining this problem Thank you ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thu, November 4, 2010 12:56:06 PM Subject: Freesurfer Digest, Vol 81, Issue 7 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: selxavg3-sess question (Douglas N Greve) 2. Re: Questions about event related processing and selxavg-sess and selxavg3-sess (Douglas N Greve) 3. Re: read data mri_vol2surf (Douglas N Greve) 4. Re: Binary masks and mri_vol2vol (Douglas N Greve) 5. Post-doctoral and data analyst positions (fMRI, MEG) (Hasson, Uri) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Nov 2010 18:57:00 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] selxavg3-sess question To: Eyal Dechter <edechter(a)mit.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1E8BC.7050606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed That version of fsfast is not version 5. The version ID for fast_selxavg3 is from april 2009. doug Eyal Dechter wrote: > Hi, I'm analyzing fMRI data using freesurfer 5.0.0. I run into the > following error when running selxavg3-sess. Any suggestions? > > Thanks, > Eyal > >************************************************************************************************************************************************* >* > > edechter@ba7:~/projects/stability/analysis$ selxavg3-sess -s tower001 > -d ../data/ -analysis tower_allruns -c unstable-stable -no-preproc > -------------------------------------------------------------- > selxavg3-sess logfile is >/u2/edechter/projects/stability/analysis/log/selxavg3-sess-bold-tower_allruns-101103112400.log >g > -------------------------------------------------------------- > ------------------------------------------- > /u2/edechter/projects/stability/data/tower001 > Wed Nov 3 11:24:01 EDT 2010 > anadir = /u2/edechter/projects/stability/data/tower001/bold/tower_allruns > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > ------------------------------------------ > ------- matlab output -------------------- > Warning: Unable to open display 'iconic'. You will not be able to > display graphics on the screen. > > < M A T L A B > > Copyright 1984-2007 The MathWorks, Inc. > Version 7.5.0.338 (R2007b) > August 9, 2007 > > Warning: Duplicate directory name: /u2/edechter/matlab. > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com > <http://www.mathworks.com/>. > > >> >> >> >> >> >> >> > /software/Freesurfer/current/fsfast/toolbox/fast_selxavg3.m > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: > fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ > outtop = /u2/edechter/projects/stability/data > Extension format = nii > ??? Undefined function or variable 'UseFloat'. > > Error in ==> fast_selxavg3 at 82 > fprintf('UseFloat = %d\n',UseFloat); > > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > edechter@ba7:~/projects/stability/analysis$ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 2 Date: Wed, 03 Nov 2010 19:05:03 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess To: Katie Bettencourt <kcrum(a)bu.edu> Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4CD1EA9F.2060403(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed The FIR does not assume a shape to the HRF but fits each point within the given time window. You might not be seeing activation for several reasons. FIRs are much less efficient than gamma functions. Also, by default, the FIR analysis gives you a sig map at each time point in the FIR, so you might be looking at the activation 1.5 sec *before* stimulus onset (so it would be a good thing not to see any activation!). Try advancing the time point from the overlay config window. You can see the map from the gamma and the timecourse from the FIR with something like tksurfer-sess -analysis fir-analysis -map-analysis gamma-analysis ... I'm not sure about the diffs with version 3. Why are you using such an old version? doug Katie Bettencourt wrote: > Hi all, > > I've been trying to analyses both an event related and block design > experiments and have noticed a couple things that are confusing me and > I would appreciate any help anyone could give me. > > 1. In trying do the event-related analysis, I'm am a bit confused by > the FIR vs Gamma analysis and the use of the time window and tprestim > in the FIR analysis. I have an experiment with 6 set size conditions > and 1 fixation condition. each trial is 6s long with a TR of 1.5 > > I have run both of these commands: > > mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat > -designtype event-related -funcstem fmc -motioncor -runlistfile > supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25 > > mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat > -designtype event-related -funcstem fmc -motioncor -runlistfile > supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20 > > > The FIR gives me a time course window, which makes me think that > perhaps that is the one I want to use, but it shows very little > activation. This data has been previously analyzed in Brain Voyager, > so I know it's not a case of the conditions not actually causing > activation, but for some reason, the FIR analysis doesn't show any. > I'm not sure if this is due to a bad time window/tprestim settings, or > something else. However the gamma fit analysis shows a bunch of > activity where I expect to see it, but no time course window. > (attached are pngs of the differences for the act_vs_fixation > comparison). > > > 2. In addition, in both the event related (gamma) and a normal block > design (different experiment) I get very different results (at least > for certain comparisons) depending on whether I use selxavg-sess (with > stxgrinder-sess for each contrast) or selxavg3-sess. The differences > are shown in the attached pngs (act_vs_fix-gamma.png (which is the > selxavg-sess and stxgrinder-sess analysis and > act_vs_fix-gamma-selxavg3). In the block design, both selxavg3 and > selxavg (+stxgrinder) give me very similar activation when comparing > two non-null conditions (ie. shape_vs_noise) but very different (and > similar to the differences in the attached pictures) activations when > comparing against the null (ie shape_vs_fix or noise_vs_fix). What am > I doing wrong here? > > Thanks for your help! > > Katie > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 3 Date: Wed, 03 Nov 2010 19:28:11 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] read data mri_vol2surf To: "Oya, Hiroyuki (UI Health Care)" <oyah(a)healthcare.uiowa.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1F00B.9060505(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed yes, use the FreeSurfer MRIread matlab command Oya, Hiroyuki (UI Health Care) wrote: > > Hello > > > > Is it possible to load the outputs of mri_vol2surf with matlab? > > > > Thank you. > > > > Hiroyuki > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 4 Date: Wed, 03 Nov 2010 19:59:52 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Binary masks and mri_vol2vol To: Andrew Ward <award(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1F778.60606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It is better to use mri_label2vol using the registration matrix for the functional. You can set the "fill threshold" to control the percent of a segmentation that must be present in a voxel to declare that voxel to be in that segment. I would not set this to 1 (ie, 100%) as this can lead to some artifacts since it just counts the number of anat voxels that land in the functional voxel. Set it to something like .85 or .9. doug Andrew Ward wrote: > Hi Freesurfers, > > I have created a binary mask of the ventricles using mri_binarize > using data from aparc+aseg.mgz. I want to resample this mask into > native functional space, but I want to include only functional voxels > that are 100% covered by by the structural mask. Because the > anatomical mask is written with voxels that are 1x1x1 and our > functional data is re-sliced at 3x3x3, there are functional voxels > that are more than 50% covered by the anatomical mask that I want to > exclude. I used the command: > > mri_vol2vol --mov brainmask.mgz --targ ventmask.nii --ing --reg > register.dat --interp nearest --o func.ventmask.nii > > This properly resampled the mask into functional space, and maintained > its binary character, but it looks to be a bit too permissive -- > although I could just be seeing things. > > Any ideas? > > Thanks for your help, > > Andrew Ward > Brigham and Women's Hospital (BBNG) > Massachusetts General Hospital (GRU) > Athinoula A. Martinos Center for Biomedical Imaging > 149 13th St., Rm 2689C > Charlestown, MA 02129 > Phone: 617-726-6211 > Fax: 617-726-5760 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 5 Date: Thu, 4 Nov 2010 04:55:56 +0100 From: "Hasson, Uri" <uri.hasson(a)unitn.it> Subject: [Freesurfer] Post-doctoral and data analyst positions (fMRI, MEG) To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <C8F77CDC.2B72%uri.hasson(a)unitn.it> Content-Type: text/plain; charset="utf-8" Applications are invited for two postdoctoral positions and one data analyst position funded by an ERC (European Research Council) Starting Grant. The research program examines the cognitive mechanisms and neural systems by which the human brain codes the recent past and predicts the immediate future. It uses neuroimaging, behavioral studies, and eye tracking methods. The ideal candidates for all positions are highlymotivated and creative individuals, capable of working independently and ingroups, who will thrive in a dynamic startup-like work environment. Prior experience with computational modeling of complex systems would be helpful. The research takes place at the Center for Mind/Brain Sciences at the University of Trento, Italy. Salaries are comparable to those offered by research institutions in the US and Europe, include benefits and health insurance, and are commensurate with training and experience. Expected starting date for all positions is Feb 1st, 2011. Interested candidates should Email a CV and a description of research interests to: Dr. Uri Hasson uri.hasson(a)unitn.it<mailto:uri.hasson@unitn.it> Center for Mind/Brain Sciences via delle Regole, 101 I-38060 Mattarello (TN) Italy Positions offered: a. Post-doctoral position (2-4 years) for fMRI research. The person will beresponsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center?s onsite 4T fMRI scanner. REQUIREMENTS: expertise with fMRI design and analysis methods and a solid background in cognitive neuroscience. HELPFUL:knowledge of functional connectivity methods including those applicable to resting state data, analysis of perfusion (ASL) data, R/Matlab programming,good understanding of UNIX. Interest in MEG methods. b. Post-doctoral position (2-4 years) for Magnetoencephalography (MEG) research. The person will be responsible for the design of several MEG studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center?s onsite MEG apparatus and 4T fMRI scanner. REQUIREMENTS: expertise with MEG techniques and a solid background in cognitive neuroscience. HELPFUL: Knowledge of coherence analysis and pattern classifier methods; knowledge of fMRI analysis techniques and the integration of fMRI and MEG data. c. Data Analyst (2 years): The data analyst will be responsible for analysis of fMRI datasets, algorithm development, programming and conducting fMRI studies, and monitoring computer hardware. This position is ideal for college graduates who are technically inclined and are considering future graduate studies in cognitive neuroscience. REQUIREMENTS: Prior experience with fMRI analysis. HELPFUL: a bachelor's degree in psychology, computer science, math, cognitive science, neuroscience, or computer science, knowledge of Italian. Experience with diverse computing environments (Linux/OSX/Windows), programming (python/perl/shell scripting, or R) and relational databases.

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Re: [Freesurfer] Freesurfer Digest, Vol 81, Issue 7
by Siti Hajar 14 Jan '11

14 Jan '11

when i ran, mri_segstats --seg fsavegagepath/hemi.fsaverage.hemi_roi_subj.mgh --in hemi.thickness.fsaverage.mgh --sum segstats-hemi_roi_subj.txt -----> in order to find the --sum segstats, error occured: Error:dimension mismatch between input volume and seg input 16342 1 1 seg 23406 1 7 but when i tried again using the old version of freesurfer, freesurfer_Linux_centos 4_x86_V4.4, it worked... "0 0 163838 163838 1 1 4 4 reporting on 2 segmentation." Can you helping me explaining this problem Thank you ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thu, November 4, 2010 12:56:06 PM Subject: Freesurfer Digest, Vol 81, Issue 7 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: selxavg3-sess question (Douglas N Greve) 2. Re: Questions about event related processing and selxavg-sess and selxavg3-sess (Douglas N Greve) 3. Re: read data mri_vol2surf (Douglas N Greve) 4. Re: Binary masks and mri_vol2vol (Douglas N Greve) 5. Post-doctoral and data analyst positions (fMRI, MEG) (Hasson, Uri) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Nov 2010 18:57:00 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] selxavg3-sess question To: Eyal Dechter <edechter(a)mit.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1E8BC.7050606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed That version of fsfast is not version 5. The version ID for fast_selxavg3 is from april 2009. doug Eyal Dechter wrote: > Hi, I'm analyzing fMRI data using freesurfer 5.0.0. I run into the > following error when running selxavg3-sess. Any suggestions? > > Thanks, > Eyal > >************************************************************************************************************************************************* >* > > edechter@ba7:~/projects/stability/analysis$ selxavg3-sess -s tower001 > -d ../data/ -analysis tower_allruns -c unstable-stable -no-preproc > -------------------------------------------------------------- > selxavg3-sess logfile is >/u2/edechter/projects/stability/analysis/log/selxavg3-sess-bold-tower_allruns-101103112400.log >g > -------------------------------------------------------------- > ------------------------------------------- > /u2/edechter/projects/stability/data/tower001 > Wed Nov 3 11:24:01 EDT 2010 > anadir = /u2/edechter/projects/stability/data/tower001/bold/tower_allruns > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > ------------------------------------------ > ------- matlab output -------------------- > Warning: Unable to open display 'iconic'. You will not be able to > display graphics on the screen. > > < M A T L A B > > Copyright 1984-2007 The MathWorks, Inc. > Version 7.5.0.338 (R2007b) > August 9, 2007 > > Warning: Duplicate directory name: /u2/edechter/matlab. > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com > <http://www.mathworks.com/>. > > >> >> >> >> >> >> >> > /software/Freesurfer/current/fsfast/toolbox/fast_selxavg3.m > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: > fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ > outtop = /u2/edechter/projects/stability/data > Extension format = nii > ??? Undefined function or variable 'UseFloat'. > > Error in ==> fast_selxavg3 at 82 > fprintf('UseFloat = %d\n',UseFloat); > > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > edechter@ba7:~/projects/stability/analysis$ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 2 Date: Wed, 03 Nov 2010 19:05:03 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess To: Katie Bettencourt <kcrum(a)bu.edu> Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4CD1EA9F.2060403(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed The FIR does not assume a shape to the HRF but fits each point within the given time window. You might not be seeing activation for several reasons. FIRs are much less efficient than gamma functions. Also, by default, the FIR analysis gives you a sig map at each time point in the FIR, so you might be looking at the activation 1.5 sec *before* stimulus onset (so it would be a good thing not to see any activation!). Try advancing the time point from the overlay config window. You can see the map from the gamma and the timecourse from the FIR with something like tksurfer-sess -analysis fir-analysis -map-analysis gamma-analysis ... I'm not sure about the diffs with version 3. Why are you using such an old version? doug Katie Bettencourt wrote: > Hi all, > > I've been trying to analyses both an event related and block design > experiments and have noticed a couple things that are confusing me and > I would appreciate any help anyone could give me. > > 1. In trying do the event-related analysis, I'm am a bit confused by > the FIR vs Gamma analysis and the use of the time window and tprestim > in the FIR analysis. I have an experiment with 6 set size conditions > and 1 fixation condition. each trial is 6s long with a TR of 1.5 > > I have run both of these commands: > > mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat > -designtype event-related -funcstem fmc -motioncor -runlistfile > supIPSruns.txt -inorm -nskip 2 -nconditions 6 -gammafit 2.25 1.25 > > mkanalysis-sess.new -analysis supIPS_loc -TR 1.5 -paradigm supIPS.dat > -designtype event-related -funcstem fmc -motioncor -runlistfile > supIPSruns.txt -inorm -nskip 2 -nconditions 6 -tprestim 2 -timewindow 20 > > > The FIR gives me a time course window, which makes me think that > perhaps that is the one I want to use, but it shows very little > activation. This data has been previously analyzed in Brain Voyager, > so I know it's not a case of the conditions not actually causing > activation, but for some reason, the FIR analysis doesn't show any. > I'm not sure if this is due to a bad time window/tprestim settings, or > something else. However the gamma fit analysis shows a bunch of > activity where I expect to see it, but no time course window. > (attached are pngs of the differences for the act_vs_fixation > comparison). > > > 2. In addition, in both the event related (gamma) and a normal block > design (different experiment) I get very different results (at least > for certain comparisons) depending on whether I use selxavg-sess (with > stxgrinder-sess for each contrast) or selxavg3-sess. The differences > are shown in the attached pngs (act_vs_fix-gamma.png (which is the > selxavg-sess and stxgrinder-sess analysis and > act_vs_fix-gamma-selxavg3). In the block design, both selxavg3 and > selxavg (+stxgrinder) give me very similar activation when comparing > two non-null conditions (ie. shape_vs_noise) but very different (and > similar to the differences in the attached pictures) activations when > comparing against the null (ie shape_vs_fix or noise_vs_fix). What am > I doing wrong here? > > Thanks for your help! > > Katie > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 3 Date: Wed, 03 Nov 2010 19:28:11 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] read data mri_vol2surf To: "Oya, Hiroyuki (UI Health Care)" <oyah(a)healthcare.uiowa.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1F00B.9060505(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed yes, use the FreeSurfer MRIread matlab command Oya, Hiroyuki (UI Health Care) wrote: > > Hello > > > > Is it possible to load the outputs of mri_vol2surf with matlab? > > > > Thank you. > > > > Hiroyuki > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 4 Date: Wed, 03 Nov 2010 19:59:52 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Binary masks and mri_vol2vol To: Andrew Ward <award(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4CD1F778.60606(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It is better to use mri_label2vol using the registration matrix for the functional. You can set the "fill threshold" to control the percent of a segmentation that must be present in a voxel to declare that voxel to be in that segment. I would not set this to 1 (ie, 100%) as this can lead to some artifacts since it just counts the number of anat voxels that land in the functional voxel. Set it to something like .85 or .9. doug Andrew Ward wrote: > Hi Freesurfers, > > I have created a binary mask of the ventricles using mri_binarize > using data from aparc+aseg.mgz. I want to resample this mask into > native functional space, but I want to include only functional voxels > that are 100% covered by by the structural mask. Because the > anatomical mask is written with voxels that are 1x1x1 and our > functional data is re-sliced at 3x3x3, there are functional voxels > that are more than 50% covered by the anatomical mask that I want to > exclude. I used the command: > > mri_vol2vol --mov brainmask.mgz --targ ventmask.nii --ing --reg > register.dat --interp nearest --o func.ventmask.nii > > This properly resampled the mask into functional space, and maintained > its binary character, but it looks to be a bit too permissive -- > although I could just be seeing things. > > Any ideas? > > Thanks for your help, > > Andrew Ward > Brigham and Women's Hospital (BBNG) > Massachusetts General Hospital (GRU) > Athinoula A. Martinos Center for Biomedical Imaging > 149 13th St., Rm 2689C > Charlestown, MA 02129 > Phone: 617-726-6211 > Fax: 617-726-5760 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ------------------------------ Message: 5 Date: Thu, 4 Nov 2010 04:55:56 +0100 From: "Hasson, Uri" <uri.hasson(a)unitn.it> Subject: [Freesurfer] Post-doctoral and data analyst positions (fMRI, MEG) To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <C8F77CDC.2B72%uri.hasson(a)unitn.it> Content-Type: text/plain; charset="utf-8" Applications are invited for two postdoctoral positions and one data analyst position funded by an ERC (European Research Council) Starting Grant. The research program examines the cognitive mechanisms and neural systems by which the human brain codes the recent past and predicts the immediate future. It uses neuroimaging, behavioral studies, and eye tracking methods. The ideal candidates for all positions are highlymotivated and creative individuals, capable of working independently and ingroups, who will thrive in a dynamic startup-like work environment. Prior experience with computational modeling of complex systems would be helpful. The research takes place at the Center for Mind/Brain Sciences at the University of Trento, Italy. Salaries are comparable to those offered by research institutions in the US and Europe, include benefits and health insurance, and are commensurate with training and experience. Expected starting date for all positions is Feb 1st, 2011. Interested candidates should Email a CV and a description of research interests to: Dr. Uri Hasson uri.hasson(a)unitn.it<mailto:uri.hasson@unitn.it> Center for Mind/Brain Sciences via delle Regole, 101 I-38060 Mattarello (TN) Italy Positions offered: a. Post-doctoral position (2-4 years) for fMRI research. The person will beresponsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center?s onsite 4T fMRI scanner. REQUIREMENTS: expertise with fMRI design and analysis methods and a solid background in cognitive neuroscience. HELPFUL:knowledge of functional connectivity methods including those applicable to resting state data, analysis of perfusion (ASL) data, R/Matlab programming,good understanding of UNIX. Interest in MEG methods. b. Post-doctoral position (2-4 years) for Magnetoencephalography (MEG) research. The person will be responsible for the design of several MEG studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center?s onsite MEG apparatus and 4T fMRI scanner. REQUIREMENTS: expertise with MEG techniques and a solid background in cognitive neuroscience. HELPFUL: Knowledge of coherence analysis and pattern classifier methods; knowledge of fMRI analysis techniques and the integration of fMRI and MEG data. c. Data Analyst (2 years): The data analyst will be responsible for analysis of fMRI datasets, algorithm development, programming and conducting fMRI studies, and monitoring computer hardware. This position is ideal for college graduates who are technically inclined and are considering future graduate studies in cognitive neuroscience. REQUIREMENTS: Prior experience with fMRI analysis. HELPFUL: a bachelor's degree in psychology, computer science, math, cognitive science, neuroscience, or computer science, knowledge of Italian. Experience with diverse computing environments (Linux/OSX/Windows), programming (python/perl/shell scripting, or R) and relational databases.

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