hi all i run recon_all on some subjects having 512x512x154 , i noticed (using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of them were cropped (more than half of the brain disappeared) after the "-nuintensity" step (nu.mgz); for one of these patients, the nu.mgz is ok but the T1.mgz produced after skullstrip is bad : the skull was largely still there on the right hemisphere.
i read in the "recon-all.local-copy" file (in the SUBJECTS_DIR/subj/scripts folder) that we must include the "-cw256" flag if the "FOV" is beyond 256x256x256 (just to be sure, is it the FOV -in mm- or the just the GRID). but when reading in the recon-all.log file, this step seems to be a default one when running "recon_all -all" command. in the recon-all.log file it is written : Original Data has (0.4883, 0.4883, 1.2) mm size and (512, 494, 154) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation thank you for your help
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