Hello, I am having difficulty with an fMRI command line program that we have run successfully in the past, but which we haven't used in ~4 months. In response to the following command lines (from a csh script):
"setenv FSL_DIR $FSLDIR source /usr/local/freesurfer/nmr-stable3-env source ${FSLDIR}/etc/fslconf/fsl.csh setenv FSLOUTPUTTYPE ANALYZE setenv SUBJECTS_DIR /cluster/ablood/1/R01_Botox cd /cluster/ablood/1/R01_Botox
preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc4 -fwhm 4 -smin fmc4 -smout fmcsm4
mkanalysis-sess.new -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -TR 2.5000 -paradigm 60_60_60_60_60_60_60.para -designtype blocked -funcstem fmcsm5 -motioncor -runlistfile runlistfile_tap_lh_long -inorm -tpef tpexclude60_60_60_60_60_60_60 -nconditions 1 -timewindow 25.0000 -gammafit 2.25 1.25 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile selxavg-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile mkcontrast-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -a 1 -c 0 stxgrinder-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -s CD_R01BTX_CTRL7_sess1 -df sessdirfile"
we get the following error messages:
ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed
In the past such an error has resulted from using the newer source environment (stable-5.1), but would always work when sourced with stable-3. I have re-run this with stable-5.1 as well, but we get the same type of error.
Any help would be much appreciated!
Thanks, Jeff