Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Error with mc-sess
by Leila Reddy 26 Nov '07

26 Nov '07

Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the message below. It then hangs. >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2007-11-13 18:44:51.464 MATLAB[6569] Process manager already initialized -- can't fully enable headless mode. I can kill the process (e.g.6569 in the example above) and it moves on to the next run, but without saving anything for the current run. Does anyone know what I can do to fix it? Thanks, Leila

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How to register a subject surface to average surface?
by Jiefeng Jiang 23 Nov '07

23 Nov '07

Hi, I used make_average_subject to create an average subject, and I want to register a subjects's pial surface to the average subject's pial surface. I used mris_make_template lh pial average lh.pial.tif to create a template, and used mris_register -curv lh.pial $SUBJECTS_DIR/average/surf/lh.pial.tif lh.pial.avg.reg but the result was a sphere. Could anyone tell me how to do the registration? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

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Re: The results of your email commands
by l.gutierrez＠ion.ucl.ac.uk 22 Nov '07

22 Nov '07

> > > > Hi, > > I fixed talairach manually (as website says), and this command is > not > > working. Could it be because now I am using the last version and I > used > > before other version? > > thanks in advance > > Leticia > > > > [leticia@triton ~/subjects]1% recon-all -all -subjid sukma > > INFO: SUBJECTS_DIR is /mounts/auto/leticia-freesurfer/subjects > > Actual FREESURFER_HOME > > /export/local/fc5_x86_64_usr2/mrtools/freesurfer/4.0.1 > > -rw-rw-r--+ 1 leticia news 1279831 Nov 22 14:37 > > /mounts/auto/leticia-freesurfer/subjects/sukma/scripts/recon-all.log > > Linux triton.nmr.ion.ucl.ac.uk 2.6.18-1.2257.fc5 #1 SMP Fri Dec 15 > > 16:07:14 EST 2006 x86_64 x86_64 x86_64 GNU/Linux > > #-------------------------------------------- > > #@# MotionCor Thu Nov 22 14:37:55 GMT 2007 > > ERROR: no run data found in > > /mounts/auto/leticia-freesurfer/subjects/sukma/mri. Make sure to > > have a volume called 001.mgz in > > /mounts/auto/leticia-freesurfer/subjects/sukma/mri/orig. > > If you have a second run of data call it 002.mgz, etc. > > See also: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > > Linux triton.nmr.ion.ucl.ac.uk 2.6.18-1.2257.fc5 #1 SMP Fri Dec 15 > > > 16:07:14 EST 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all exited with ERRORS at Thu Nov 22 14:37:55 GMT 2007 > > > > >

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POSTDOCTORAL FELLOWSHIP IN SPEECH PERCEPTION AND THE STRUCTURE AND FUNCTION OF HUMAN AUDITORY CORTEX
by David L. Woods 21 Nov '07

21 Nov '07

POSTDOCTORAL FELLOWSHIP IN SPEECH PERCEPTION AND THE STRUCTURE AND FUNCTION OF HUMAN AUDITORY CORTEX A postdoctoral fellowship is available in Martinez, CA (in the San Francisco Bay Area) to study the relationship between age-related changes in speech perception and anatomical and functional changes in human auditory cortex. Speech processing will be tested with nonsense syllables and sentences and correlated with tests of basic auditory discrimination abilities and auditory short-term verbal memory. Subject with impaired speech processing will then undergo PC-based adaptive training designed to improve speech processing in noise and force beneficial neuroplastic changes in auditory cortex. Brain structure will be imaged using multimodal structural brain imaging (including high-resolution T1, diffusion tensor, and magnetization transfer imaging) and analyzed using advanced cortical surface mapping as well as automated techniques to analyze subcortical structures and white matter tracts. In selected subjects, functional activations to speech and non-speech stimuli will be studied using fMRI. The job involves close collaboration with international scientists, graduate students, and post-docs. Job Availability: Immediate. Job duration: 2-4 years. Salary: $40,000-$65,000 depending on experience. QUALIFICATIONS. Successful candidates should have a strong background in auditory perception, physiology and/or anatomy (PhD or MD required), a good publication record, familiarity with Windows and Linux operating systems, and some programming experience. Knowledge of psychophysics, neuropsychology, and neuroimaging methods including ERPs, fMRI, or TMS is desirable. US citizenship preferred. Interested candidates should email a C.V., letter of intent, and the names of three references to: Professor David L. Woods, Dept. of Neurology, UC Davis and VANCHCS (127E), 150 Muir Rd., Martinez CA 94553. Email: <file:///dlwoods@ucdavis.edu>dlwoods(a)ucdavis.edu.

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Re: [Freesurfer] Folding Index question
by Graham Wideman 21 Nov '07

21 Nov '07

[Bruce wrote] >sounds reasonable to me, but we should call it something else (normalized >FI/CI?) Yes, dividing out area does look like a first step, justified by the way the per-vertex values are calculated. This gives the result units of mm^-2, which maybe has an interpretation something along the lines of "folds per square millimeter". But, as noted in off-list emails, I think it would be premature to release an "NewFI" revised only in this way, because it suggests that the other principles of FI are sound, which I'm currently not confident about. Rudolph and I are in the process of reconciling our understandings of how the FI calculations currently behave, and whether that was what was intended (and probably whether what was intended is even a useful idea). Anyhow, hopefully the outcome of this will be better calcs implementing something useful, (with documentation of intent and usefulness :-). Graham

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Re: [Freesurfer] Folding Index question
by Rudolph Pienaar 20 Nov '07

20 Nov '07

Hi Graham - First off, your observation that the FI seems correlated with area is completely correct. I'm not sure if you have the FS source code? Anyway, looking at the relevant code in 'mrisurf.c', the MRIScomputeCurvatureIndices(...) function pretty much computes the folding index (fi) as fi += area * Kmax * (Kmax - Kmin) ; and then, once having summed over the surface, simply divides by *pfi = fi / (4.0*M_PI) ; In essence, this is Van Essen's Folding index -- although I personally do have some issues with it. First of all, Van Essen normalizes his measure with 1/4/pi, indicating that the 1/4pi is the "integral for a cylinder the length of which equals its diameter). I seem to think this integral should be (1/2pi)^2, i.e. 1/4/pi^2. Either way, this is merely a fixed constant and doesn't change the behaviour. And irrespective of the 1/4pi or not, the measure is a strict function of "size", or more accurately, the radius of curvature. Since the curvatures run as the inverse of radius, the curvature values in small sulci/gyri can dominate the 'Folding Index', even if they are 'folded' exactly the same as larger sulci/gyri. In fact, there is nothing really related to 'folding' per se in the measure, so it is arguably something of a misnomer - but I fear I am digressing. I know Bruce originally wrote the FI into FS, but based on this quick re-analysis, I'm kind of thinking that we should normalize the fi (and ici for that matter) with the area overwhich each measure measure is computed... *pfi = fi / (4.0*M_PI) / areaCounted; This makes potentially more sense and removes the area dependency. What do you think, Bruce? -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] Folding Index question (fwd)
by Rudolph Pienaar 19 Nov '07

19 Nov '07

On Monday 19 November 2007 09:07, Graham wrote: > 1. DVE's description of the FI calc, which it looks like FS implements > (assuming FS's k calcs are faithful -- that code is hard to follow.) Yep - that the code can be hard to follow. Still, you can assume that FS's k calcs are faithful. But on deeper reflection, the FI calculation in FS has a core area-dependency in the code that probably should be normalized out. > > a) Cylindricallity of gyri and sucli do not contribute equally -- one is > emphasized and the other suppressed. (KMax,Kmin = (5,0) --> FI of 25, vs > KMax,Kmin = (0, -5) --> FI of 0; I think these are the gyral and sulcal > versions of the same shape, right?) > Ok - I suspect you need to think of Kmax and Kmin (also known as the principle k1 and k2 curves) in absolute terms when comparing. The sign really only indicates if the surface is curving "inwards" or "outwards", and doesn't convey comparative magnitude. So, in the case where one of the principle curves is -5 and the other is 0, k1=-5 and k2=0 (Kmax=-5 and Kmin=0), resulting in the same values for gyri and sulci. > b) Certain moderate saddle shapes contribute *negatively*, though the > *extreme* saddle shapes contribute *zero*. This I can't immediately comment on, but even if there is contribution from a saddle shape (i.e. k1 should be approximately k2), so the FI should be close to zero. Switching tracks, you might be interested in the re-vamped 'mris_curvature_stats', which has kind of morphed into the main curvature measure tool in FS. This tool now computes several principle curvature functions on a given surface (optionally saving each as a curvature file), and also determines area- and vertex-normalized integrals for the different functions. Furthermore, the functions and integrals are also computed for only positive and negative curves (or Gaussian curvatures) separately, so sulci and gyri are easily distinguishable. One of the measures is a so-called "sharpness function", which is conceptually related to Van Essen's FI: Sharpness = (k1-k2)^2 Van Essen FI = abs(k1)*(abs(k1)-abs(k2)) The sharpness function gives an indication of how sharply folded a gyrus or sulcus is. What version of 'mris_curvature_stats' are you running? It has seen some active development over the past summer, so you might not have the newest version. Give me a shout if you'd like the current dev version. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Error with selxavg-sess
by Leila Reddy 19 Nov '07

19 Nov '07

Hi, I encountered an error with "selxavg-sess -sf sessid -df sessdir -analysis loc-sm3". Looking through the archives I found that others had errors with selxavg-sess but the errors don't seem to be exactly the same as mine. Please let me know if you have any suggestions on how to get this to work. My log file is pasted at the bottom of this email. I use the PowerPC version of freesurferv4.0.1 --------------------------------------------------------------------- FREESURFER_HOME: /Software/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.10.0 Power Macintosh --------------------------------------------------------------------- Thanks a lot! Leila selxavg-sess log file $Id: selxavg-sess,v 1.18 2007/01/09 22:41:18 nicks Exp $ uid=1132(lreddy) gid=1132(lreddy) groups=1132(lreddy), 1185(kraskov), 1152(rodri), 1090(psycho) /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006 /Software/freesurfer/fsfast/bin/selxavg-sess -sf sessid -df sessdir -analysis loc-test Darwin wagner.klab.caltech.edu 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc Sun Nov 18 20:20:37 PST 2007 selxavg: Command not found. ------------------------------------------- /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006 Sun Nov 18 20:20:37 PST 2007 -------------------------------------------------------- /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold selxavg2 -TR 2.0000 -parname loc.para -o loc-test/h -i 011/f -i 021/f -i 025/f -cfg /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg -ipr 3 -pomnibus loc-test/omnibus/fsig -fomnibus loc-test/omnibus/f -------------------------------------------------------- here --- Parsing Config File: /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 Logfile is loc-test/h_sxa.log matlab file is /tmp/sxa_6634.m ----------- Matlab file -------------- % Matlab file for selxavg2 Sun Nov 18 20:20:38 PST 2007 % This file may be deleted % /tmp/sxa_6634.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '2.0000', '-parname', 'loc.para', '-o', 'loc-test/h', '-i', '011/f', '-i', '021/f', '-i', '025/f', '-cfg', '/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg', '-ipr', '3', '-pomnibus', 'loc-test/omnibus/fsig', '-fomnibus', 'loc-test/omnibus/f'); if(r==0) fmri_touch('/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold/loc-test/selxavg.ok.6634'); end exit qoe; ----------------------------------- ------------------------------------------ ------- 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. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2006 The MathWorks, Inc. Version 7.2.0.283 (R2006a) January 27, 2006 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Duplicate directory name: /home/lreddy/matlab. > In path at 113 In startup at 380 In matlabrc at 216 >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40 2007/01/15 02:29:36 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = bhdr Checking Parameters nslices = 32 AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 011/f 2 021/f 3 025/f Input Pardigm File List 1 011/loc.para 2 021/loc.para 3 025/loc.para Output Volume loc-test/h F Omnibus Volume loc-test/omnibus/f Sig Omnibus Volume loc-test/omnibus/fsig TR 2.000000 TER 2.000000 Total Window 30 PreStim Window 6 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 1 2.25 1.25 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 ExtReg File mcextreg NExtReg 3 ExtRegOrthog 0 firstslice 0 nslices 32 nyqreg 0 SynthSeed = 0 Conditions Found (4): 1 2 3 4 Run 1: 32 32 32 32 Run 2: 32 32 32 32 Run 3: 32 32 32 32 Slice 0, 9.29485e-05 -------------- First Pass (Accumulation), 0.000672511 Run 1/3, 0.00150713 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 011/f Run 2/3, 3.50438 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 021/f Run 3/3, 6.90937 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 025/f Second Pass (Residual Error Estimation), 9.85656 ??? Error using ==> svd NaN or Inf prevents convergence. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg at 239 c = cond(SumXtWX); >> ??? Undefined function or variable 'r'. >> ------------------------------------------ ERROR: fast_selxavg() failed\n ----- End forwarded message -----

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Reading mris_smooth output using Matlab
by Kim Mouridsen 19 Nov '07

19 Nov '07

Hi, We have segmented hippocampus using Freesurfer, and want to generate a surface which can be read into matlab. We use mri_tesselate and mris_smooth. However, the resulting file can not be read into matlab using read_surf. The error we get is ??? Undefined function or variable "vertex_coords". Error in ==> read_surf at 77 vertex_coords = reshape(vertex_coords, 3, vnum)' ; It seems the 'magic' number is 16777213, whereas only 16777214 and 16777215 are supported in read_surf.m How can we read the result of mris_smooth into matlab? Thanks! Kim.

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Folding Index question
by Graham Wideman 16 Nov '07

16 Nov '07

Folks: We're wondering about how FS's "folding index" corresponds to Van Essen's calculation (J Neurosci, 1997 Sept 15). In particular, do the FI values for each region factor out the area of the region or not. When we plot them the FI values look extremely correlated to area, but that doesn't make sense for an index. Ultimately we're wanting to know how to aggregate FIs for individual parcellations into larger regions. Thanks, Graham

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