Hi Wan,

you need to find out what the actual direction cosines are. I think we make a default assumption for analayze files and add the actual voxel dimensions.

Bruce

On Thu, 14 Apr 2005, Wan Park wrote:

Unfortunately I only have img/hdr files.

when I put mri_info I have this message:

[ash:14725/mri/orig] wpark% ls 14725.hdr 14725.img [ash:14725/mri/orig] wpark% mri_info 14725.img INFO: analyzeRead(): found 1 files for /usr/local/freesurfer_package/freesurfer subjects/14725/mri/orig/14725.img

---

INFO: could not find /usr/local/freesurfer_package/freesurfer/subjects/14725/mr /orig/14725.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default) INFO: if not valid, please provide the information in /usr/local/freesurfer_pac age/freesurfer/subjects/14725/mri/orig/14725.mat file

---

Volume information for 14725.img type: analyze3d dimensions: 256 x 256 x 124 voxel sizes: 0.7812, 0.7812, 1.5000 type: SHORT (4) fov: 0.000 xstart: 0.0, xend: 0.0 ystart: 0.0, yend: 0.0 zstart: 0.0, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degre s nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.000 voxel to ras transform: -0.7812 0.0000 0.0000 100.0000 0.0000 0.7812 0.0000 -100.0000 0.0000 0.0000 1.5000 -93.0000 0.0000 0.0000 0.0000 1.0000 [ash:14725/mri/orig] wpark%

I know that doing mri_convert -iid x_r x_a x_s -ijd y_r y_a y_s -ikd z_r z_a z_s I can change the orientation. In this case it would be mri_convert -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 14725.img .

My questions:

1. Are these the "default" values that the mri_convert use if I do not

specify anything? (mri_convert 14725.img .) 2) If I want to change, the possible values are -1 0 and 1?

Thank you very much.

Wan