Freesurfer September 2010

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[Fwd: Re: Talairach afd error]
by Oya, Hiroyuki 03 Sep '10

03 Sep '10

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Talairach afd error
by Oya, Hiroyuki 03 Sep '10

03 Sep '10

Dear all, recon-all failed at the talairach stage. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux hiroyuki-desktop 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC 2010 x86_64 GNU/Linux In what circumstances do we see this? T1 STRUCTURAL looks OK . Any comment would be appreciated. Hiroyuki

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dicom help
by Gabriel Go.Es. 02 Sep '10

02 Sep '10

Hello FreeSurfers I'm trying to convert some dicom images, but some of them apparentely FS just does not recognize them as dicom images, even when their extention is *.dcm, I'm sending you an example, one of the dicom series, in case any one can helpme disguising the problem, i'll really appreciate it. I'm using FS v4.2 Kind Regards Gabriel

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optseq2 - nominal ideal XtX
by Leo Fernandino 02 Sep '10

02 Sep '10

Hi Doug and all, In the output summary of optseq2, does the absolute value of the efficiency of nominal ideal XtX matter when evaluating your design? Specifically, I'm experimenting with different TR durations, and it looks like shorter TRs give me lower efficiency values, but these values are comparatively closer to the respective eff of the nominal ideal XtX. How should I interpret this? Thank you, Leo

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retinotopy in Freesurfer 5.0
by Katie Bettencourt 02 Sep '10

02 Sep '10

I had a couple questions relating to how to perform retinotopic analysis and view the results in the new Freesurfer 5.0 distribution (bear with me, previous I was using Freesurfer 4.0.2, so there's probably a bunch of changes that are confusing me). 1. I was able to create a new analysis with mkanalysis-sess, and compute the stats with selxavg3-sess. But I'm a bit confused on displaying the data. When I use tksurfer-sess I can see the sig map (which isn't really helpful for determining regions) or use the -map angle command and see something that looks a bit like retintopy but in the heat overlay display type (sorry, not sure the correct terminology here) instead of the standard color wheel. When I try to change the overlay display settings to color wheel and complex it becomes all a single color (green). Perviously I also had to change the phase encoding display settings to 2.0 plus some offset (which I can't actually do right now do to a bug I'm having), but you would at least still see some color differences with the 1.0 phase setting, and I'm not getting any of that. What am I doing wrong? 2. Previously, you could load the brain with tksurfer (not tksurfer-sess) and load data through overlays and loading the real and imag .w files created with paint-sess. I know that now paint-sess isn't needed, but when I try to load the real.nii and imag.nii or even angle.nii this doesn't work. Can you only load retinotopic data through tksurfer-sess command line now? 3. When I try to change the fthresh in the command line, it seems to read it, but then overwrite it with retinotopic data. Is there no way in the command line to change the fthresh value? 4. In the analysis example I was following you had to create a separate analysis for lh and rh, why is this? thanks! Katie

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Re: [Freesurfer] mris_anatomical_stats
by Krish Subramaniam 02 Sep '10

02 Sep '10

On Sep 2, 2010, at 2:49 PM, corinna bauer wrote: > Thank you, that seems to have done the trick. > > On Thu, Sep 2, 2010 at 2:13 PM, Krish Subramaniam <krish(a)nmr.mgh.harvard.edu > > wrote: > Hi Corinna > > I think most likely it's the division operator ( / ) you used in the > line > > > gwratio.vol = gray.vol/white.vol; > > Element-wise division in MATLAB is achieved by a ./ . I think the > line should be > > > gwratio.vol = gray.vol./white.vol > > You could debug it by placing a > > size(gwratio.vol) > > immediately following the line and see if it agrees with the sizes > of gray.vol and white.vol > > See this : http://www.mathworks.com/access/helpdesk/help/techdoc/ref/mldivide.html > for more information > > -Krish > > > On Sep 2, 2010, at 1:48 PM, corinna bauer wrote: > > Do you have any idea as to what may have gone wrong? Both files that > went into creating the ratio have dimensions: 151243 x 1 x 1. > In matlab I did this: > > rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; > paths=dir([rootdir,'/*']); > > num=numel(paths) > for ii=428:num > fprintf('----- Processing %i of %i -----\n', ii, length(paths)); > if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && > ~ > strcmp > (paths > (ii > ).name,'..')); > pathgray=fullfile(rootdir,paths(ii).name,'mri/ > rh.white.projfrac.pos35.mgh'); > gray = MRIread(pathgray); > pathwhite=fullfile(rootdir,paths(ii).name,'mri/ > rh.white.projdist.neg1.mgh'); > white = MRIread(pathwhite); > > gwratio = gray; > gwratio.vol = gray.vol/white.vol; > > > pathratio=fullfile(rootdir,paths(ii).name,'mri','rh.gwratio.mgh'); > MRIwrite(gwratio, pathratio); > > > On Wed, Sep 1, 2010 at 4:43 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > Something went very wrong with the creation of that file. It only > has one voxel/vertex. > > doug > > corinna bauer wrote: > Volume information for /home/freesurfer4.4.0/subjects/corinna/1057/ > mri/lh.gwratio.mgh > type: MGH > dimensions: 1 x 1 x 1 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: FLOAT (3) > fov: 1.000 > dof: 1 > xstart: -0.5, xend: 0.5 > ystart: -0.5, yend: 0.5 > zstart: -0.5, zend: 0.5 > TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip > angle: 8.00 degrees > nframes: 1 > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = > 58340.0000 > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a > = 11.5254 > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s > = 0.0000 > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1.0000 0.0000 0.0000 58340.5000 > 0.0000 0.0000 1.0000 11.0254 > 0.0000 -1.0000 0.0000 0.5000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 0.0000 0.0000 58340.5000 > -0.0000 -0.0000 -1.0000 0.5000 > -0.0000 1.0000 -0.0000 -11.0254 > 0.0000 0.0000 0.0000 1.0000 > > > On Wed, Sep 1, 2010 at 2:07 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > can you run > > mri_info > /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh > > and send us the output? > > > On Wed, 1 Sep 2010, corinna bauer wrote: > > mris_anatomical_stats -t > /home/freesurfer4.4.0/subjects/corinna/1057/mri/lh.gwratio.mgh > 1057 lh > > > On Wed, Sep 1, 2010 at 1:59 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>wrote: > > > what is your full command line? > > On Wed, 1 Sep 2010, corinna bauer wrote: > > Then I get this error: > > > ERROR: number of vertices in > /home/freesurfer4.4.0/subjects/corinna/1057/mri/ > lh.gwratio.mgh > does not > match surface (1,116670)structure is > "/home/freesurfer4.4.0/subjects/corinna/1057/surf/ > lh.white" > number of vertices = 116670 > total surface area = 76860 mm^2 > total gray matter volume = 0 mm^3 > average cortical thickness = 0.000 mm +- > 0.000 mm > average integrated rectified mean curvature = 0.131 > average integrated rectified Gaussian curvature = 0.112 > folding index = 2190 > intrinsic curvature index = 223.0 > > > On Wed, Sep 1, 2010 at 1:29 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > > wrote: > > > Try using the full path to the file > > > > > On Sep 1, 2010, at 12:16 PM, corinna bauer > <corinnab83(a)gmail.com > <mailto:corinnab83@gmail.com>> wrote: > > Hi Bruce, > When I use the -t flag, I get this message in the > output: > > mghRead(1057/mri/lh.gwratio.mgh, -1): could not > open file > > I tried: > mris_anatomical_stats -t 1057/mri/lh.gwratio.mgh > 1057 lh > > Corinna > > On Tue, Aug 31, 2010 at 8:40 AM, Bruce Fischl << > fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi Corinna, > > > the gwratio.mgh is a scalar field over the > surface, *not* a surface > (i.e. > it has no topology information). Try: > > mris_anatomical_stats -t lh.gwratio.mgh > > and the rest as normal. Note that it will > report the values as > "thickness" > > cheers > Bruce > > > > On Mon, 30 Aug 2010, corinna bauer wrote: > > I am trying to get an output with average > gray/white ratio values for > > each > segmentation. I tried using the > gwratio.mgh file as the input for > mris_anatomical_stats, but got the > following error message: > > reading input surface > /home/freesurfer4.4.0/subjects/1057/surf/ > lh.gwratio.mgh... > ERROR: MRISread: file > '/home/freesurfer4.4.0/subjects/1057/surf/ > lh.gwratio.mgh' > has 0 > vertices! > > Any insight? > > > > The information in this e-mail is intended > only for the person to whom > it > is > addressed. If you believe this e-mail was sent > to you in error and the > e-mail > contains patient information, please contact > the Partners Compliance > HelpLine at > <http://www.partners.org/complianceline> > http://www.partners.org/complianceline . If > the e-mail was sent to you > in > error > but does not contain patient information, > please contact the sender and > properly > dispose of the e-mail. > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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mris_anatomical_stats
by corinna bauer 02 Sep '10

02 Sep '10

I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices! Any insight?

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FSFAST TUTORIAL
by Danny Kim 02 Sep '10

02 Sep '10

Hello all, I've recently downloaded Freesurfer 5 and was going through the FSFAST tutorial. I keep on getting an error saying when I run "preproc-sess -s mgh-101.1 -fwhm 5 -per-run": -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ fmri setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects Darwin copernicus.bcricwh.lan 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 /Applications/freesurfer/fsfast-tutorial/my-study /Applications/freesurfer/fsfast/bin/preproc-sess -s mgh-101.1 -fwhm 5 -per-run Thu 2 Sep 2010 11:03:13 PDT instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain mgh-101.1 Template ----------------------------- mktemplate-sess -s mgh-101.1 -d /Applications/freesurfer/fsfast-tutorial/my-study -fsd bold -update Session: /Applications/freesurfer/fsfast-tutorial/my-study/mgh-101.1 ---------------- Thu 2 Sep 2010 11:03:13 PDT find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found Anyone managed to encounter this problem in the past? Thanks in advance for your help! Best Regards, Danny Kim BC Children's Hospital

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getting polar/eccen retinotopy maps into matlab
by Finnegan Calabro 02 Sep '10

02 Sep '10

Hi Doug et al, I'm trying to import the polar and eccentricity maps resulting from a retinotopy analysis into Matlab for some additional manipulation. Specifically, what I'd like is to get something like the output from: surf-sess -s sessid -a rtopy -retinotopy polar/eccen -flat as polar and eccentricity values that I can use to compare to activation from another task (i.e. what are the polar visual field coordinates for all surface locations with significant activation in the other task). The surf-sess command above works and the rest of the field sign analysis looks good, so I think the analysis all went fine, but I'm not sure which files contain the data I'm looking for (seems like map-real/imag-?h.w, but if so, I'm not clear on how to combine the real and imaginary parts). Thanks! Finn

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intensity correction error
by Mareen Kussatz 02 Sep '10

02 Sep '10

Hi to all, thanks for your help, we could solve the autorecon2 problem! there is another problem with autorecon1... ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running mincresample (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) ERROR: nu_correct Darwin RK2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 The Intensity correction ist not running, after we had an error at talairach transformation step. I went to tkregister2 (talairach is not ok- and started again recon-all, finally get that error??? best Mareen -- GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 €/mtl.!* http://portal.gmx.net/de/go/dsl

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Freesurfer September 2010