Freesurfer

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30086 discussions

reading PET in Matlab
by Rafa x 03 Sep '10

03 Sep '10

Dear Freesurfers, I’m trying to obtain in matlab the PET value of each vertex of the cortex from one freesurfer subject. To calculate it, first I do the coregister with: bbregister -–mov PETimage.nii –-t2 –-s subjectName –-init-fsl –-reg register.dat I have checked the result and it is provides perfect corregister between the PET and MRI. Then I calculate the PET in the cortical surface with: mri_vol2surf -–mov PETimage.nii –-reg register.dat –-hemi ?h –projfrac 0.5 –-interp nearest –-o PETSurface.mgh I load it with tksurfer like an overlay. It shows the variability of the PET activity across the cortex without problem. At last I extract the parameters in Matlab with: [vol, M, mr_parms, volsz]=load_mgh(PETSurface.mgh) The problem appears when I compare the values of PET in some vertices. The most of the vertices checked (not all) doesn’t have the same value in tksurfer and matlab (obtained with vol(numberOfVertex)). The values in tksurfer and matlab are similar (in the same magnitude order) but are not equal. Maybe I’m taking a wrong way of obtain the PET activity in Matlab. I hope that someone can help me. Thank you all in advance, Rafael.

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Re: [Freesurfer] OSX bug in getrunlist
by Douglas N Greve 03 Sep '10

03 Sep '10

Yes, you are correct! I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist copy it into $FREESURFER_HOME/fsfast/bin doug Jason Webster wrote: > Hey Doug, > > I am just trying out 5.0 on OSX and stumbled into a bug in getrunlist. > > The command: > set RunList = (`find -maxdepth 1 -name "[0-9][0-9][0-9]"`); > needs to be replaced with: > set RunList = (`find . -maxdepth 1 -name "[0-9][0-9][0-9]"`); > lest it throws: > > find: illegal option -- - > 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 > > > > ~Jason > -- 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

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

03 Sep '10

talairach.xfm file is as below: ---------------------- MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 1.37266099 0.20895453 0.18430687 13.98477840 0.46526164 0.99459654 -3.29530478 68.71842194 -0.81687593 0.73364604 3.47314310 -136.09573364 ; ------------------------ This looks awful. an image is also attached. Thanks again. On Fri, 2010-09-03 at 09:36 -0400, Bruce Fischl wrote: > can you post these to the list so others can answer? Did you check the > talairach.xfm with either tkmedit or tkregister2? > > On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: > > > Hi Bruce, > > > > Bringing up the image with tkmedit, directions are correct. > > And I have not done any process in Analyze format. > > > > Thank you. > > > > > > > > > > > > On Fri, 2010-09-03 at 09:24 -0400, Bruce Fischl wrote: > > > >> Hi Hiroyuki, > >> > >> can you check to make sure that the direction cosines are correct? Bring up > >> the orig.mgz and make sure that coronal is coronal, sagittal is sagittal > >> and horizontal is horizontal. Did this data go through analyze at any time? > >> > >> cheers > >> Bruce > >> > >> > >> On Fri, 3 Sep 2010, Oya, Hiroyuki wrote: > >> > >>> 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 > >>> > >>> > >>> > >>> > >>> > >> > >> > >> 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 . 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. > >> > > > > > > //***********************// > > Hiroyuki Oya, M.D. > > Assistant Professor, > > Department of Neurosurgery, > > University of Iowa, > > 200 Hawkins drive, Iowa City, > > IA, 52242-1061, USA > > tel:1-319-353-8452 > > e-mail: hiroyuki-oya(a)uiowa.edu > > fax:1-319-353-6605 > > > > > > //***********************// Hiroyuki Oya, M.D. Assistant Professor, Department of Neurosurgery, University of Iowa, 200 Hawkins drive, Iowa City, IA, 52242-1061, USA tel:1-319-353-8452 e-mail: hiroyuki-oya(a)uiowa.edu fax:1-319-353-6605

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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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