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
Hi Jeff, if you're going to use version 3, then you need to use an older version of FSL. Currently, you have FSLDIR pointing to the current version. Probably the "current" version changed over the last few months. if you look in /usr/pubsw/packages/fsl, you'll see all the versions we have. I don't know which one you need, maybe just go to the 2nd most recent one. Why are you using version 3? doug
On 07/18/2012 12:42 PM, jwaugh@nmr.mgh.harvard.edu wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jeff, if you're going to use version 3, then you need to use an older version of FSL. Currently, you have FSLDIR pointing to the current version. Probably the "current" version changed over the last few months. if you look in /usr/pubsw/packages/fsl, you'll see all the versions we have. I don't know which one you need, maybe just go to the 2nd most recent one. Why are you using version 3? doug
On 07/18/2012 12:42 PM, jwaugh@nmr.mgh.harvard.edu wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
jwaugh＠nmr.mgh.harvard.edu