hi, i am using bshort files. should i try bfloat? thanks, margaret On Thu, 4 Nov 2004, Doug Greve wrote:
> > 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 > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [EMAIL PROTECTED] > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > [EMAIL PROTECTED] > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > _______________________________________________ > > Freesurfer mailing list > > [EMAIL PROTECTED] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > [EMAIL PROTECTED] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
