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.
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