Re: [Freesurfer] mris_anatomical_stats

It could be that the input files (eg, mghrh.white.projfrac.pos35) were created, then the subject was edited (which would change the number of vertices), but the input files were not re-created. Check the creation dates on the files.

doug

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/mghrh.white.projfrac.pos35.'); 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@nmr.mgh.harvard.edu mailto:greve@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@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
    <mailto:fischl@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@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
           <mailto:fischl@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@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
                   <mailto:fischl@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@gmail.com
    <mailto:corinnab83@gmail.com>
                       <mailto:corinnab83@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@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
                       <mailto:fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>>>

                       fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>
                       <mailto:fischl@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@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>