SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?

It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?

doug

Margaret Duff wrote:

Hi, I have 12 runs of functional data I am trying to convert to FSFast formats and then preprocess. I have been using mri_convert to make my .img files into bshorts. However mri_convert makes only 30 files when my folders originally contained 37 or 73 files. Is this what it is supposed to do? I am also then trying to run preproc-sess on these files but i keep getting an error during the motion correction of the first run. it says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf sessid -df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank you so much, Margaret Duff

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