Hi,
I was trying to preprocess some data with the option of slice time correction but preproc-sess exited with the following error:
preproc-sess -sf sessid -df sesspar -rlf runlistfile -sliceorder odd - fwhm 8 -update
... ... -------------------- INFO: set hdr.hist.orient to -1 /Users/eiji/exp/myFS slicetimer -i /Users/eiji/exp/FS_classic_oddball_2009/090407_K/bold/ 004/tmp.76874/in.img -o /Users/eiji/exp/ FS_classic_oddball_2009/090407_K/bold/004/tmp.76874/out.img --ocustom=/ Users/eiji/exp/FS_classic_oddball_2009/090407_K/bold/004/tmp.76874/ saof.dat ERROR:: Unrecognised value (ANALYZE) of environment variable FSLOUTPUTTYPE Legal values are: NIFTI, NIFTI_PAIR, NIFTI_GZ, NIFTI_PAIR_GZ ERROR: mc-sess failed
It turns out that I have FSL 4.1 installed on my system and FSL 4.1 does not support outputting of Analyze files anymore (http://www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html ). I suppose this error will not occur if one sticks with the FSL package (3.2?) that comes bundled with freesurfer.
So I thought the "least effort" solution would be to prevent preproc- sess from trying to output in Analyze.
Below are 3 changes I had to do in fsfast/bin/stc.fsl to make it work:
1) Comment out line #158 in stc.fsl
#setenv FSLOUTPUTTYPE ANALYZE
2) Edit line #159 from
set outtmp = $tmpdir/out.img
to
set outtmp = $tmpdir/out.nii.gz
3) Edit line #176 from
set cmd = (mri_convert -it analyze4d $outtmp $outfunc)
to
set cmd = (mri_convert -it nii $outtmp $outfunc)
I want to make sure I am not unknowingly messing up with some later stage in preproc-ses, if you find something like that, please let me know!
Thanks a lot!
Eiji
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