Hi Margaret,
is the input volume bshort or bfloat? I've never been able to get the AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter.
doug
Margaret Duff wrote:
Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
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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