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> 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>>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> 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>> 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>> 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.
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