Hello,
I had installed FSL 5.0.11 and was having this issue as well. I followed the instructions about removing the fslpython directory and rerunning the installation.
This did not result in these executables being placed in $FSLDIR/bin
What did this actually do? Are these executables placed somewhere else? Or how is this functionality being replaced with fslpython?
The exectuables in $FSLDIR/bin some executables in $FSLDIR/bin still reference them as if they should be there, whereas others simply rely on $PATH finding them:
$ grep immv *
bet: ${FSLDIR}/bin/immv ${OUT}_tmp_unbiased_forskull_skull ${OUT}_skull
feat_gm_prepare: ${FSLDIR}/bin/fslecho "cd ${f}/reg; $FSLDIR/bin/fast -R 0.3 -H 0.1 -o grot highres; $FSLDIR/bin/immv grot_pve_1 highresGM; /bin/rm grot*; $FSLDIR/bin/fslmaths highresGM -s $struc_smoothing highresGMs; \c" >> ${OUT}.log/featseg1
featregapply: immv $TMPNAM reg_standard/$out
fsl_anat: run $FSLDIR/bin/immv ${T1} ${T1}_fullfov
fsl_anat: run $FSLDIR/bin/immv ${T1}_biascorr ${T1}_biascorr_init
fslchfiletype: $FSLDIR/bin/immv $newfile ${oldfile}TMP
fslchfiletype: $FSLDIR/bin/immv ${oldfile}TMP $oldfile
fslvbm_2_template: $FSLDIR/bin/immv ${g}_brain_pve_1 ${g}_GM" >> fslvbm2a
mainfeatreg: runCommand $9 "${FSLDIR}/bin/immv ${out}_fieldmaprads2epi_shift unwarp/FM_UD_fmap2epi_shift"
mainfeatreg: runCommand $9 "${FSLDIR}/bin/immv ${out}_fieldmap2str unwarp/FM_UD_fmap_mag_brain2str"
mainfeatreg: immv ${1}2${2} ${1}2${2}_linear
quasil: immv data aslraw
quasil:immv aslraw_even aslcontrol
quasil: immv calib/mean_T1t calib/T1t
quasil: immv calib/mean_g calib/g
quasil: immv calib/mean_M0t calib/M0t
tbss_1_preproc: $FSLDIR/bin/immv $f origdata
tbss_deproject:$FSLDIR/bin/immv ${IN}_tmp_deprojected ${IN}_to_all_FA
verbena: immv brain_mask mask
Thanks for any information you can provide to help me get this working correctly.
Cicada Dennis
Indiana University
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