Dear Free Surfers,
I wonder if something went wrong with transitioning FS-FAST and/or unpacksdcmdir from 4.5 to 5.0. Our functional analysis stream is set to work in 4.5 and it was working fine. However, since the default version was changed to 5.0, our analyses have stopped working despite that we source /space/freesurfer/nmr-stable4-env
We receive multiple errors (see ERROR 1 and ERROR 2 below) that start already at preprocessing (ERROR 1 below). For example, functional data from Bay 4 that was unpacked with unpacksdcmdir before the version shift goes through preprocessing just fine (even today), whereas if I re-unpack the exact same raw data the preprocessing fails.
Details:
cd /space/avml/3/users/bletham/ADA_fMRI/AD003/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT AD003_FSvs4.5
nmr-std-env # this takes us to version 5.0 of course so we also give
source /space/freesurfer/nmr-stable4-env
****************** **** ERROR 1: **** ******************
preproc-sess -sf subjectname -df sessdir -fwhm 6 -sliceorder siemens -inorm -force
... some messages ...
>> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Error using ==>
fmri_svbfile Too many output arguments.
Error in ==> fast_svbslice at 71 err = fmri_svbfile(yslice,fname);
Error in ==> MRIwrite at 83 err = fast_svbslice(mri.vol,fstem,[],outbext,bmri);
ERROR: output not created ERROR: mc-sess failed
****************** **** ERROR 2: **** ******************
For data that was unpacked before the version change, now when we try to run analyses under vs 4.5 we also receive another type of error at selxavg3-sess that seems to be related to version numbers:
... Computing CES Magnitude AV8VT-REST J=13 ------------- Computing CES Magnitude Saving h.dat to /autofs/space/avml_003/users/bletham/ADA_fMRI/AD003/bold/FIRsm6pf2_taumax20/h.dat ??? Reference to non-existent field 'Version'.
Error in ==> fmri_svdat3 at 35 if(hd.Version == 2)
Error in ==> fast_selxavg3 at 1039 fmri_svdat3(fname,hd);
ERROR: fast_selxavg3() failed\n
Any suggestions? Anything and everything of course most welcome!
Best regards,
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.