Hi:

Your description of the problem looks to me like there's some trouble with the interpretation of the 1404 mm dimension. It seems very unlikely that you have a scan that actually covers 1404 mm, so there must be a problem here.

I would advise reading the header of the scan, which might require some program to read and interpret the header for you.

Perhaps the header actually contains sensible information, such as:

1404 slices at 0.2 mmm --> ~ 280 mm field of view in that direction

or

304 slices (or some other sensible number) instead of 1404.

Anyhow, if you see this, it would suggest that the scan is OK, but FreeSurfer is having trouble loading it. A possible strategy in that case is to load the scan into some other software, resample to a grid closer to 1 mm grid, and trim/pad to make it 256 x 256 x 256.

Software which might help there is AFNI. Also MRICro (Chris Rorden) might be useful, and even my GWRawMRIView for inspecting what your dealing with.

http://grahamwideman.com/gw/brain/tools/gworc/index.htm

Hope that helps,

Graham

At 1/25/2008 11:32 AM, you wrote:

Hi, I have a problem about which image is the best to run. I had ran the 1.5T data in freesurfer. Because the contrast of the 1.5T data was too bad, I use the 3T data and rerun again. When I run, it says the warning,

WARNING ============++++++++++++++++++++++++======================== The physical sizes are (1404.00 mm, 256.00 mm, 256.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 1404 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). =====================++++++++++++++++++++++++===============

This problem confused me. What can I do? Could you tell me what image is freesurfer I can run and get the best results? (about dimension¡K. )

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