Hi Yawu what was the full recon-all command line? What is your input format? If all else fails you can mri_convert your input volume nifti or mgz and override what is in the header (e.g. mri_convert -iks 1 ...)
cheers Bruce On Fri, 6 Feb 2015, Liu Y wrote: > 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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
