Dear Experts, When I run recon-all -cw256 -s problemcase -all, the program seems not able accurately to recognize the voxel size in this problematic case, in other cases there is no problem. The program gave a warning like this:
WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 338 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++=============== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz... TR=8.08, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels. Data is conformed to 1 mm size and 338 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz... **************************************** ERROR! FOV=338.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Then I checked the orig.mgz, the image was re-scaled (stretched) in left-right direction, and could not see the left and right boundaries of the brain. The program said that the Original Data has (1, 1, 2) mm size, but actually the voxel size is 1*1*1 mm3. The freesurfer version 5.3, Ubuntu 12.04 Thanks, Yawu
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