oh sorry, /space/troy/1/users/FREESURFER/SM2S1_fsfast/func/SM2S1 and i was trying to run it on the bold folder. could it have to do with my matlab startup? i thought i modified it correctly when i started using the program. but as i look back through my command window i see a warning that my startup.m file might be wrong. can you tell me everything that needs to be included in that file? thanks so much, margaret
On Mon, 8 Nov 2004, Doug Greve wrote: > > No, bshort should work fine. Can you be more specific as to where the > data are? There are lots of possibilities under /space/troy ... > > doug > > > Margaret Duff wrote: > > > > 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
