Hi Cicada,
These utilities are now installed separately from the main FSL
installation. They are installed into the fslpython miniconda
environment during the post-installation stage and, after a successful
installation, can be found in:
$FSLDIR/fslpython/envs/fslpython/bin/
The executables in this directory are accessed via sym-links in
$FSLDIR/bin/, e.g.:
$FSLDIR/bin/imcp -> $FSLDIR/fslpython/envs/fslpython/bin/imcp
Cheers,
Paul
On 22/04/2019, Cicada Dennis <[log in to unmask]> wrote:
> 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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