Hi Corinna,

sorry, I'm not sure what's going wrong. Can you try loading that volume calling load_mgh directly? Make sure the filename is exactly right. It's hard to tell with all the carriage returns in your email.

cheers Bruce

On Fri, 4 Jun 2010, corinna bauer wrote:

When I run mri_info I get:

Volume information for /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac.35.mgh type: MGH dimensions: 23334 x 1 x 5 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 23334.000 dof: 0 xstart: -11667.0, xend: 11667.0 ystart: -0.5, yend: 0.5 zstart: -2.5, zend: 2.5 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 = 5.5017 : 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 : /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 11672.5020 0.0000 0.0000 1.0000 9.0254 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 11672.5020 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -9.0254 0.0000 0.0000 0.0000 1.0000

On Fri, Jun 4, 2010 at 9:58 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

if you run mri_info on the .mgh file does it return reasonable looking values?

On Fri, 4 Jun 2010, corinna bauer wrote:

Hi Bruce,

...

I am having trouble getting my .mgh files to open in MRIread. I get the following error message.

ERROR: could not open /home/freesurfer4.4.0/ subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh for reading ERROR: loading

/home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh as MGH ??? Attempt to reference field of non-structure array.

Error in ==> gwRatio at 24 gwratio.vol = gray.vol / white.vol;

here's my .m file

function gwRatio

rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; paths=dir([rootdir,'/*']);

numel(paths) num = numel(paths);

for ii = 1:num if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && ~strcmp(paths(ii).name,'..'))

  graypath=

fullfile(rootdir,paths(ii).name,'mri/lh.white.projfrac35.mgh'); whitepath = fullfile(rootdir,paths(ii).name,'mri/lh.white.projdist.neg1.mgh'); outpath = fullfile(rootdir,paths(ii).name,'mri/lh.gwratio.mgh');

  fprintf('----- Processing %i of %i -----\n', ii, num);
  fprintf('gray: %s\n', graypath);
  fprintf('white: %s\n', whitepath);
  fprintf('out: %s\n', outpath);

  gray = MRIread(graypath);
  white = MRIread(whitepath);
  gwratio = gray;
  gwratio.vol = gray.vol / white.vol;
  MRIwrite(gwratio, outpath);

end end

corinna

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